A tearful crowd in Liverpool sang You'll Never Walk Alone and releasing blue and purple heart-shaped inflatables into the sky above Liverpool, where Alfie spent his short life.
One supporter was heard shouting "I love you Alfie!" during a countdown to the release, while others chanted the embattled toddler's name.
The emotional vigil paid tribute to the terminally ill infant, who has been in a coma for the past 16 months.
After months of conflict between Alfie's parents, doctors and courts, Alfie's life support machine was finally switched off on Monday.
Devastated dad Tom Evans, 21, shared his passing with the world, writing on the Alfie's Army support group: "My gladiator lay down his shield and gained his wings at 02:30… absolutely heartbroken… I LOVE YOU MY GUY".
Alfie's mum Kate James wrote: "Our baby boy grew his wings tonight at 2:30 am. We are heart broken. Thankyou everyone for all your support".
Alder Hey Children's Hospital released a statement offering their "heartfelt sympathy" to Alfie's family while adding that their "thoughts are with them" after a "devastating journey."
Tributes quickly began to pour for the tot, who had an incurable brain condition, on social media after his parents confirmed the devastating news at about 6.20am.
The Pope took to Twitter to talk of his sorrow, saying: "I am deeply moved by the death of little Alfie. Today I pray especially for his parents, as God the Father receives him in his tender embrace."
Alder Hey Children's Hospital's statement
- "We wish to express our heartfelt sympathy and condolences to Alfie's family at this extremely distressing time.
- "All of us feel deeply for Alfie, Kate, Tom and his whole family and our thoughts are with them.
- "This has been a devastating journey for them and we would ask that their privacy and the privacy of staff at Alder Hey is respected."
Sir Alan Sugar said: "RIP Alfie Evans . Sad day for his parents who fought so hard for him."
Tory MP and leader of the House of Commons, Andrea Leadsom, tweeted: "So very sad to hear that Alfie Evans has passed away. My thoughts are with his parents and family who must be devastated.
"Grateful thanks to the hospital staff who did all they could for him in such terribly difficult circumstances".
Sky News' Kay Burley added simply: "RIP Alfie Evans"
BBC Breakfast's Dan Walker said:" Very sad to hear about the death of little Alfie Evans. I hope his family are able to find some sort of peace after such a painful & public few weeks."
England WAG Becky Vardy added: "This morning heaven gained an angel. Alfie Evans you stole my heart and the hearts of so many!
"May you rest in peace little man. Thinking of you, Tom and Kate! You did your little champ proud."
How brave Alfie battled his illness
9 May 2016 – Alfie is born in Liverpool to parents Tom Evans and Kate James.
1 December 2016 – Alfie is taken to Alder Hey Children's Hospital after suffering seizures. He will spend the next 12 months there.
11 December 2017 – The hospital and family disagree over Alfie's treatment, with his parents saying that the hospital applied to the High Court to remove parental rights and withdraw ventilation.
19 December 2017 – The High Court case begins with Mr Justice Hayden saying he will make a decision on what is best for Alfie.
1 February 2018 – A hearing begins at the High Court in Liverpool in which lawyers acting for the hospital claim further treatment for Alfie is unkind and inhumane.
2 February 2018 – One of Alfie's doctors tells the judge there is "no hope" for the youngster, who is in a semi-vegetative state from a degenerative neurological condition doctors have not been able to definitively diagnose.
20 February 2018 – Mr Justice Hayden rules in favour of the hospital and accepts medical evidence that further treatment would be futile.
6 March 2018 – Three Court of Appeal judges uphold the decision of Mr Justice Hayden.
20 March 2018 – Supreme Court justices refuse the couple permission to mount another appeal.
28 March 2018 – The European Court of Human Rights also rejects a request from the family to intervene.
16 April 2018 – Alfie's parents argue he is being wrongly "detained" at Alder Hey and make a habeas corpus application. Judges at the Court of Appeal in London rule against them.
18 April 2018 – Mr Evans flies to Rome and meets with Pope Francis.
20 April 2018 – The Supreme Court rules against Alfie's parents for a second time.
23 April 2018 – The ECHR rejects a last-ditch appeal. Supporters storm the hospital. Alfie is granted Italian citizenship. His life support is turned off at 9.17pm.
24 April 2018 – Alfie is still breathing on his own and has had oxygen and water, his father tells supporters.
25 April 2018 – Alfie's parents lose their appeal to take the tot to Italy for further treatment.
26 April 2018– Supporters of Alfie hold a candlelit vigil for the child at the Vatican as his father calls for demonstrations outside the hospital to end
28 April 2018 – Alfie dies five days after doctors turn off his ventilator
TV chef James Martin added: "RIP Alfie Evans"
Boxer and fellow Liverpudlian also tweeted his condolences to the little lad saying: "RIP Alfie Evans… A brave little soldier all the way to the end… Thoughts are with his mother & father today.. #RIPAlfieEvans."
Model Danielle Lloyd, also from Liverpool, wrote: "Heartbroken this morning to wake up to the news @alfiesarmy has past away what a strong little boy he was now he will be watching over all that helped him.
"Having children myself I can’t imagine just how the past months years have been for his family Rest in peace angel."
Alfie died after receiving treatment at Liverpool's Alder Hey children's hospital where he had been in intensive care for more than a year suffering from a mystery brain condition.
The battling tot had surprised medics by breathing unaided with just oxygen, milk and water since life-support was withdrawn at 9.17pm on Monday.
His parents had asked well-wishers to pray as they kept a bedside vigil and posted pictures of him sleeping on mum Kate's chest as he clung to life.
Alfie's plight touched millions around the world and drew a personal intervention from Pope Francis as his parents lost a high-profile legal battle to keep him alive.
The head of the Vatican’s Bambino Gesu Pediatric Hospital even travelled to Liverpool in a bid to get the sick tot flown to Italy.
Supporters held protests in London, Belfast, Warsaw and the US after judges refused to let Alfie go to a hospital in Italy.
On Thursday evening supporters held a candlelit vigil at the Vatican – as Tom called for protests outside the hospital to end so Alfie's final days could be "dignified".
Emotions got high and supporters were in tense stand offs with police as they campaigned outside the hospital building.
But Tom pleaded with them to “return back to your everyday lives” after accepting the campaign was over and deciding to focus instead of trying to take Alfie home to die in peace.
He thanked medics for their "dignity and professionalism" and added: “Together we recognise the strains that recent events have put upon us all and we now wish for privacy for everyone concerned.
“In Alfie’s interests we will work with his treating team on a plan that provides our boy with the dignity and comfort he needs."
Tom also told Alfie's Army: "We are very grateful and we appreciate all the support we have received from around the world, including from our Italian and Polish supporters, who have dedicated their time and support to our incredible fight."
He also praised partner Kate for sustaining him and their son, saying: "Alfie’s fought through the night the last two nights because he’s been lying on her chest nonstop.
"And him and his mum have become closer now more than ever before."
He added: "I cannot explain how blessed I am to have Alfie and Kate in my life. That's what keeps me fighting".
On Wednesday night Kate posted a poignant clip of their sleeping son with the words: "My whole entire world I love you so much baby boy".
Another clip showing her stroking his face attracted 1.2 million Facebook views in 11 hours.
After Tom's plea, the protest site outside Alder Hey was all but abandoned as supporters left behind balloons and posters vowing never to give up the fight to keep Alfie alive.
Liverpool NHS staff had been warned to hide their uniforms after being targeted with abuse online and amid rowdy scenes at the hospital.
Alfie was born on May 9, 2016, but missed developmental milestones and began suffering seizures after a chest infection.
He was placed on life support at Alder Hey in December 2016, where he stayed for the next 16 months of his tragically short life.
Last year his parents began a bitter legal fight with the hospital about his care.
Doctors said brain scans showed his frequent seizures had destroyed most of his brain tissue.
A High Court judge agreed it was not in Alfie's best interests to continue treatment and he should be allowed to die.
Tom and Kate hoped to take him to hospitals offering to treat him in Italy and Germany but repeated challenges to the Appeal Court, Supreme Court and European Court of Human Rights all failed.
Lawyers launched a fresh appeal after Alfie's life support was switched off but three top judges refused another bid to take him to the Vatican's Bambino Gesu clinic.
The case had echoes of the plight of Charlie Gard, who died a week short of his first birthday after a high-profile legal battle against Great Ormond Street hospital last year.
His parents raised £1.2million for experimental treatment in the US but judges said it was futile.
Chris Gard and Connie Yates have backed a campaign for "Alfie's Law" to give parents more say over hospital care.
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