"Years back I had a relationship, and I had absolutely no idea in the world he was going to do this... he threw himself under a truck," Sir Elton said. "There was so much grief."
Mr Furnish told The Sunday Telegraph that the lover, whom he declined to name, had taken his life because he was traumatised by the clash between his Christianity and his sexual inclinations.
"He was so tortured by the conflicting views between his sexuality and his strong religious beliefs that he chose to take his own life," said Furnish, whom Sir Elton "married" in a ceremony at Windsor Guildhall on the first day that civil partnerships could be performed in England. "It is very sad indeed."
Mr Furnish, a former advertising executive, added that "out of respect" for the dead man's family he would not name him.
Sir Elton, who has a fortune estimated at £175 million, said his grief had inspired him to provide financial support for a stage play that opened in New York last week.
The couple are producers of the play, Next Fall, which documents the relationship between two homosexual men: one a young Christian from the southern states of America; the other, a non-believer. One of the men suffers an accident.
"It's the right timing for this," said Mr Furnish. "The religious divide between Right and Left has gotten wider, and so the rights of gay people never got back to where it was heading."
Sir Elton added: "Look, we all need love. We all have the same fears and insecurities. We should all be allowed to be free."
The disclosure by the flamboyant musician is likely to provoke much speculation about the identity of his late lover.
Sir Elton was known for his sexual promiscuity during the 1970s and 1980s when he struggled with addiction to alcohol and illegal drugs, and suffered from bulimia.
On Valentine's Day 1984, the musician, who has claimed that everyone is bisexual to a degree, caused widespread surprise by marrying Renate Blauel, German recording engineer, When they divorced four years later.
Sir Elton said he was "comfortable" being homosexual.
Mr Furnish said of Sir Elton, whose first sexual experience had been with a woman, the secretary Linda Woodrow: "For many, many years, he had a lot of demons stored away; a lot of skeletons in his closet. And he's learnt that a happy and burden-free life comes out of being honest."
Among Sir Elton's ex-lovers was John Reid, his former manager, with whom he was involved in an unsuccessful £8 million High Court battle in 2000.
During the case, in which the singer claimed that Reid mishandled his business affairs, he admitted spending £30 million in less than two years, including almost £15,000 a month on flowers.