Masato Uchishiba was sentenced to five years in prison for the assault on a teenage member of a college judo club he was coaching, a court official said, after she drunkenly fell asleep in a Tokyo hotel.
Uchishiba, 34, was feted as a national hero after bringing home a gold medal from the 2004 Athens Olympics, an achievement he repeated at the 2008 Beijing Games.
Prosecutors said the incident occurred in September 2011, when the women's judo club from Kyushu University of Nursing and Social Welfare had been on a visit to Tokyo.
After a night of drinking and karaoke, the teenager, whose exact age was not given but who was believed to have been 18 or 19 at the time, fell asleep in her hotel room and awoke to find Uchishiba raping her.
"When she became aware, she resisted by saying, 'What are you doing? Stop.' But he turned up the volume of the television and covered her mouth with his hand," prosecutors said, according to NHK.
The victim is not being identified publicly because of the nature of the crime.
Married Uchishiba pleaded not guilty and maintained throughout the trial that the sex with the teenage student had been consensual.
Uchishiba today said in court he would appeal the decision.
The verdict comes after a torrid week for judo, in which the coach of the national women's team resigned after admitting claims that he beat his athletes with a bamboo sword were "more or less true".
Ryuji Sonoda, who took the team to the London Olympics, acknowledged allegations of violence against his charges, including face-slapping and verbal abuse.