More than 11,000 people died or disappeared during Argentina's "Dirty War", a systematic crackdown on leftists and other opponents of the government. Human rights groups say the number is closer to 30,000.
The ruling was the latest by courts that have found new impetus for bringing former officials to justice after Argentina's supreme court - at the urging of Nestor Kirchner, the former president - struck down two amnesty laws in 2005 that shielded them from human rights abuse charges.
In its ruling, the court ordered Bignone to serve out his sentence in an ordinary jail.
But lawyers for the former leader, who is now under house arrest, are likely to appeal that he not be held in jail due to health reasons.
Bignone was the last of four military de facto presidents in Argentina under the military government, which ended in 1983 amid a deep economic crisis and a defeat in the war against Britain over the Falkland Islands.
Many of the military government's top leaders are under house arrest on charges of kidnapping babies born to mothers held in captivity during military rule.