Jorge Rafael Videla is reported to have died from natural causes in prison.
The general was jailed in 2010 for the deaths of 31 dissidents during the 1976-83 military dictatorship, of which he was overall leader until 1981.
Up to 30,000 people were tortured and killed during this period, in a campaign known as the “Dirty War”.
Gen. Jorge Rafael Videla had been sentenced to life in prison for torture, murder and other crimes in 1985, but was pardoned in 1990 under an amnesty given by the president at the time, Carlos Menem.
In April 2010, the Supreme Court upheld a 2007 federal court move to overturn his pardon.
Eight months later Jorge Rafael Videla was found “criminally responsible” for the torture and deaths of 31 prisoners and jailed for life.
Most of the left-wing activists were taken from their cells in the central city of Cordoba and shot dead shortly after the military took power.
The army said at the time that they were killed while trying to escape.
Gen. Jorge Rafael Videla was one of 30 members of the security forces charged with the murders.
Last year, he was also convicted of overseeing the systematic theft of babies from political prisoners.
At least 400 babies are thought to have been taken from their parents while they were held in detention centres.
More than 100 children given for adoption to military or police couples have since been reunited with their biological families.
A court in Buenos Aires sentenced Jorge Rafael Videla to 50 years in prison, while another ex-military leader, Reynaldo Bignone, received 15 years for his alleged role in the crime.
In an interview with an Argentine journalist last year, Jorge Rafael Videla said the crackdown he oversaw was the price Argentina had to pay in order to remain a republic.
“War, by nature, is cruel,” he said.
“An internal war, between brothers, is especially cruel.”
Jose Miguel Vivanco, director of Latin America for US-based Human Rights Watch, said Jorge Rafael Videla presided over one of the region’s cruellest repressions in modern times.
“He was arrogant to the end and unwilling to acknowledge his responsibility for the massive atrocities committed in Argentina,” he said.
“Many of the secrets of the repression will die with him.”
Argentina’s Nobel Peace Prize winner Adolfo Perez Esquivel told Reuters news agency: “Death has brought an end to his physical existence but not what he did against the people.”
The head of the Grandmothers of the Plaza de Mayo, an association that works to uncover the real identities of the stolen children, described Jorge Rafael Videla as a “bad man”.
“I’m reassured that a discredited man has departed this world,” said Estela de Carloto in a statement to local media.
Jorge Rafael Videla was born in 1925, the son of an army colonel.
In 1976, he and two other military leaders staged a coup against President Isabel Peron, the widow of former leader Juan Domingo Peron.
Argentina’s dictatorship:
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