The flypast took place at the end of flight Lieutenant Kenneth Bellamy’s funeral on Wednesday.
Mr Bellamy died on Friday, 12 August and his family wished to honour his service, fighting against Imperial Japanese pilots to defend Australia.
His daughter Karen Hewitt said the service, at St Michael’s Church , was exactly what her dad had always wanted.
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She said:”It was always one of his wishes that a Spitfire fly over his funeral, we always laughed and said that he wouldn’t see it though.
“But a lot of people have gone to a lot of trouble to organise this for him.”
The Spitfire made around four circuits of the city before flying in above the church on its final approach.
Born in Lincoln in 1923 Mr Bellamy Joined the RAF in 1942 at the age of 17, soon becoming a commissioned officer.
After completing his training in the United States and Canada he was dispatched with other pilots as part of RAF squadron 54 in 1943.
The relocation was ordered by the then Prime Minister Winston Churchill as part of efforts to strengthen air defences at Darwin in Northern Australia.
Fears mounted as the Empire of Japan rapidly expanded from 1937 onwards, occupying large areas of China and the far eastern colonial holdings of Britain, France and Holland.
Only the previous year the largest attack ever mounted against mainland Australia was carried out, with areas such as Darwin heavily bombed.
After serving in Australia Mr Bellamy was eventually demobbed in 1946.
And he returned home the same year and met his wife Peggy. The couple had two children Anthony Bellamy and Karen Hewitt.
As a civilian Mr Bellamy found work with high street retailer Burton.
Eventually working his way up to the position of area manager he relocated to Wakefield, later moving to Co-op menswear, where he worked until retiring in 1988.
In his spare time he was a volunteer helping organisations including Wakefield Hospice and Meals on Wheels.
The funeral took place at St Michael’s Church with family and members of the 54 RAF squadron, including Air Marshall Sir Roger Austin.