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Halil Ibrahim Dinçda?’s case has become a symbol of discrimination against gays and lesbians in the largely conservative and overwhelmingly Muslim Turkish society.
A court in Istanbul fined the TFF 23,000 Turkish Lira (£5,300) in material and moral compensation over its treatment of Mr Dinçda?, 38, whose licence to referee was revoked on the grounds of his sexuality.
He had been a football referee in Trabzon for 13 years but after he came out in 2009 his licence was revoked and he lost his job as a radio presenter.
The TFF had argued he was unfit for the role since he was exempt from military service on the grounds of his homosexuality.
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"This lawsuit was a case in favour of all people who suffered injustice and discrimination," Mr Dincdag told the Diken online news website.
"Winning this case was really something very important. The court has now confirmed that my fight was a right.
"I hope that this decision sets a precedent for similar cases. This is a victory."
Mr Dinçda? and his lawyer Firat Soyle said that they would appeal for their full initial demand of 110,000 Turkish Lira ($38,000).
"We are happy that justice has been done but we are going to appeal regarding the figure to be paid," the lawyer said, quoted by Turkish media. "Given the moral and material damages suffered, it is a small figure.
"December 29 2015 is a victory in the fight against homophobia in football and also a victory for the LGBT movement in Turkey," he added.
"We have to break the taboo on football over homophobia with this decision."
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