In handing down his ruling, judge Tomonao Onizawa said the court "cannot trust at all" claims by Uchishiba that he had consensual sex with the student, Kyodo news agency reported.
Uchishiba, 34, who gold in the 66-kilogram class at the Athens and Beijing Olympics, is expected to appeal.
The judge said the woman's accusation of sexual assault while she was asleep was credible given that she could not stand up on her own after drinking too much alcohol at a restaurant before the incident. Prosecutors accused Uchishiba of intoxicating the student in order to take advantage of her inability to resist.
Uchishiba was arrested in December 2011 over the rape allegation and barred from all judo activities by the All Japan Judo Federation in January 2012.
The ruling is the latest in a series of embarrassing incidents to hit judo.
On Thursday, Japan's women's judo coach Ryuji Sonoda resigned over accusations he physically abused female judoka at a training camp before the London Olympics.
Japan failed to win a gold medal in men's judo at London. The only gold for the nation that invented the sport was won by Kaori Matsumoto in the women's 57-kilogram division.