Then president Carlos Menem granted the pardons to "close a sad and black stage of Argentine history".
The decision, five years after both were sentenced to life in a military prison, sparked widespread protests.
Videla was originally found guilty of 66 homicides, the torture of 93 other people and the illegal confinement of more than 300.
Massera was convicted of three killings, the torture of 12 people and the illegal confinement of 69 dissidents.
Announcing its decision on Wednesday, the court did not rule on pardons granted to other convicted military chiefs, Orlando Agosti, Roberto Viola and Armando Lambruschini, who have since died.
The current government led by Nestor Kirchner has reopened hundreds of human rights cases since a 2005 Supreme Court ruling that struck down 1980s laws granting blanket amnesty to people involved in official repression.
Videla, who was de facto president until 1981 and is now aged 81, is currently under house arrest related to other cases.
On Tuesday an Argentine court denied Videla's extradition to Germany for prosecution in the 1977 killing of a German activist.
Spain also seeks his and Massera's extradition.
After a stroke in 2002, Massera won a court ruling that he was mentally unfit for trial on charges of stealing babies born to jailed dissidents.
The military surrendered power to an elected civilian government in December 1983 after the country's disastrous defeat to British forces in the Falklands War.