"The charges have been proved beyond all reasonable doubt," Cesar San Martin, the chief judge, said.
It marks the first time a democratically elected Latin American leader has been found guilty of rights abuses.
Fujimori has said that he will appeal the verdict and his sentence.
Clashes at trial
|Security was tight outside the police base
where the trial was held [Reuters]
Al Jazeera's Mariana Sanchez, at the trial in Lima, said that while Fujimori had initially proved popular with Peruvians, widely perceived as clamping down on economic chaos and the Shining Path group.
But corruption scandals and the trial had led most people to believe he was guilty of the charges levelled against him, she said.
Fujimori, who had repeatedly denied the charges, appeared calm in live televised pictures of the courtroom, listening intently as the verdict was read out and pausing frequently to take notes.
Outside the base where the trial was held, both supporters and opponents of Fujimori fought each other on the street with sticks, fists and rocks before being dispersed by riot police, AP news agency reported.
About 30 relatives of victims had clashed with about 500 Fujimori supporters, although no injuries were immediately reported.
The verdict related to two massacres, the first committed on November 3, 1991 when a group of armed and masked soldiers burst into a party in the Lima suburb of Barrios Altos, killing 15 people, including an eight-year-old boy.
Several months later, nine university students and their professor were rounded up by the same "La Colina" squad, taken to a deserted area of the city, and executed with shots to the back of the head.
Fujimori was also found guilty in relation to the kidnapping of a Peruvian journalist working for a Spanish newspaper and a businessman, both critics of his government.
Fujimori fled to Tokyo in 2000 while still president amid a deepening corruption scandal involving his then-intelligence chief, Vladimiro Montesinos, and sent his resignation letter by fax from his hotel.
Japan considered Fujimori, whose parents were Japanese, to be a national and refused to extradite him.
He stayed there for the next five years before flying to Chile in 2005, where he was arrested as he prepared a new presidential bid.
Two years later he was extradited to Peru and found guilty in December 2007 on charges of abuse of power over the illegal removal of sensitive audio and video tapes from Montesinos's apartment.