Timothy Gee was jailed for eight years when he was convicted at Leeds Crown Court in 2001. He fell ill and died from an undiagnosed blood cancer the following year.
Always maintaining his innocence, Mr Gee launched two unsuccessful appeals before his death. He has now been cleared by the Court of Appeal.
Campaigners have described the case as one of the worst miscarriages of justice they have seen.
Gail Saunders, of the campaign group Falsely Accused Carers and Teachers, said: "It is an appalling example of the extraordinary difficulties faced by individuals who are accused of abuse many years after the alleged offence."
Mr Gee's 88-year-old mother Molly has been awarded more than £62,000 costs by the court after battling to clear her son's name. As part of that bid, she contacted the Criminal Cases Review Commission, which asked a leading psychiatrist to report on the girl – now aged 26 – who had accused Mr Gee of rape.
While the study cast doubt on the girl's mental state, it emerged that she had also made similar accusations against another man, whose conviction was quashed earlier this year.
Mrs Gee said: "It all boiled down to one girl's word against his, and the jury believed her. That's all it took to send my son to prison and it has left me very angry and grief stricken. I don't think anyone should have to work alone with a child – it's just too easy for an allegation like this to be made."
Mr Gee, from Lindley, Huddersfield, taught brass instruments for 25 years in Kirklees and Calderdale before he was accused of raping and indecently assaulting a pupil in a Huddersfield school in 1989.
He died aged 55 in August 2002, a month after his second appeal failed.
Overturning Mr Gee's conviction, Lady Justice Smith said that experts now believed the girl's statements to be "unreliable."