Darryl Gee, who was born with a crippling back condition, was jailed in 2001 despite an almost complete lack of evidence to corroborate his accuser's claims, which related to an alleged incident more than a decade earlier.
The music teacher protested his innocence but died in his cell of an undiagnosed cancer of the blood, 18 months into an eight-year sentence.
This week campaigners described the case as one of the worst miscarriages of justice they had seen after the Court of Appeal in London quashed his conviction.
It comes as the Westminster government introduces new guidance to schools designed to speed up investigations into alleged abuse of pupils, a move which unions say will reduce the risk of innocent teachers being publicly smeared by false allegations.
Chris Keates, general secretary of teachers' union the NASUWT, said: "This is an extreme and tragic illustration of the consequences of malicious allegations, and underlines the need for these new procedures."
Mr Gee's 88-year-old mother, Molly, who was awarded pound;62,493 costs by the appeal court - the money she spent attempting to clear her son's name - said it should act as a warning to other teachers.
"It all boiled down to one girl's word against his, and the jury believed her," she said. "That's all it took to send my son to prison and it has left me griefstricken but very angry. I don't think anyone should have to work alone with a child. It is just too easy for an allegation like this to be made."
Mr Gee, a supply teacher who taught brass instruments, was found guilty at Leeds crown court in January 2001 following an accusation that he raped and indecently assaulted a pupil in a Huddersfield classroom in 1989.
Calderdale council, Halifax, concerned that he may have been in contact with up to 400 youngsters in the area during his 30-year career, even set up a telephone helpline for former pupils who might need counselling.
Mr Gee died aged 55 in August 2002, just a month after a second appeal against his conviction failed. Seven months later his father, who is said to have descended into depression, also died.
His conviction was quashed when his mother alerted the Criminal Cases Review Commission, which in turn asked a leading psychiatrist to compile a dossier on his accuser. The report cast doubt on her mental state. It also emerged that the girl, now aged 26, made similar allegations against another teacher, whose conviction was quashed at a retrial in February this year.
Lady Justice Smith, the appeal court judge, said the outcome of Mr Gee's original trial "might well have been different" had the evidence come to light earlier. Between 1993 and 2003, police investigated 1,742 allegations of child abuse made against teachers, but just 69 were convicted.