Gisela Ortiz, whose brother was killed at La Cantuta University in 1992 as Fujimori's squads hunted for presumed left-wingers, said: "For the first time, the Peruvian justice system rose to the occasion in this historic fight against impunity."
Human rights groups also welcomed the verdict.
"After years of evading justice, Fujimori is finally being held to account for some of his crimes," said Maria McFarland, a senior Americas researcher at Human Rights Watch, who was in the courtroom for the announcement.
Fujimori could still be pardoned by Alan Garcia, the current Peruvian president, if he loses his appeal, our correspondent said.
Fujimori's daughter, Keiko, a congresswoman considering a run for the presidency in 2011, called for peaceful protests against what she said was an "unjust" verdict.
"They've won the battle but not the war," she told the AFP news agency.
The sentence, and Fujimori's age, mean he will almost certainly spend the rest of his life in prison.
It marks the first time a democratically elected Latin American leader has been found guilty of rights abuses.
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, supporters and opponents of Fujimori fought each other on the street with sticks, fists and rocks before being dispersed by riot police.
About 30 relatives of victims had clashed with about 500 Fujimori supporters, although no injuries were 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.
|Supporters and opponents of Fujimori fought before being dispersed by police [AFP]
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 their heads.
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, 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.
He was extradited to Peru two years later 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.