The Ministry of Defence (MOD)'s Joint Casualty and Compassionate Centre (JCCC) organised the service, which was led by the Reverend (Dr) Group Captain Giles Legood, Deputy Chaplain in Chief (Operations), RAF.
Personnel from RAF Halton in Buckinghamshire carried his coffin.
The graveside ceremony was attended by family members, including niece Shelagh Coates from Stamford in Lincolnshire.
A church service followed at the Cathedral of San Mauro in Cavarzere.
The crash site of what was believed to be Spitfire PT 410 was excavated, and human remains were found in October 2017.
An RAF pilot's wings and Warrant Officer rank insignia were among the artefacts recovered.
The JCCC conducted research and proved the only pilot and Warrant Officer missing who died over land was Harry Coates.
Additional evidence was provided by parts of his Spitfire, on which could be seen remnants of the serial number (PT 410).
A DNA match with a profile from a member of Harry's family was proven after forensic samples were taken from his remains in November 2018.
Louise Dorr of the JCCC said: “It is a great privilege to be here today to see WO Coates finally laid to rest, particularly in the presence of so many of his family.
"I’m delighted that we have been able to identify him and bring his particular story to an end.”
The Revd Dr Giles Legood said:
“All of us chosen to represent the RAF have an important part to play in this significant occasion.
"I am honoured to be able to show, through the words of the funeral service and through our actions, that every member of the RAF is remembered and valued as a child of God”.
Ms Coates said: “We are very grateful to Romagna Air Finders for finding the missing plane of our uncle – John Henry Coates, otherwise known to family as uncle Harry, and the remains of his body after he went missing in March 1945.
"It is a great honour for us to finally put him to rest in the Padua War Cemetery today.
"Unfortunately, the find was too late for his youngest brother, my father Frank, who died in 2015, and his sister Betty, who died in 2016.
"But his burial has been attended by many of his relatives from great, great nephews and nieces through to immediate nephews and nieces.”