The senators voted 43-7 with one abstention and 21 lawmakers absent to support the proposal, which was passed last week by the lower House of Congress.
The final congressional approval marked a victory for human rights groups pressing for a national re-examination of the 1976-83 dictatorship and highlighted a new political will by Argentines under new President Nestor Kirchner to probe human rights abuses during the so-called Dirty War era.
The decision brought raucous applause from visitors' balconies and shouts of "Ole! Ole! Ole!" from human rights activists.
Women wearing scarves denoting the Mothers of the Plaza de Mayo, who are still seeking an accounting for those missing, filled the galleries.
Some held up crinkled black-and-white photos of victims who had disappeared during the seven-year period during which leftist opponents were hunted down, kidnapped off the streets, tortured in clandestine centers and made to disappear in a systematic state crackdown on dissidents.
While the Senate vote gave final legislative approval to scrapping the laws, observers said the Supreme Court will likely have the final decision on the laws. Supporters of the laws are expected to appeal to the justice system to maintain them.
At issue was the fate of Argentina's "Full Stop" and "Due Obedience" laws, enacted in 1986 and 1987 respectively. Those laws effectively ended human rights trials after the dictatorship.
Some 9,000 people were officially reported as dead or missing during those the seven-year dictatorship, but human rights groups estimated the number could be as high as 30,000.
Following Argentina's dictatorship, many ranking military officers were tried on charges of abduction, torture and execution of suspected leftist opponents of the regime. They were imprisoned in 1985, angering the military.
A series of uprisings and mutinies by disgruntled officers against Argentina's newly restored democracy left elected civilian Raul Alfonsin no choice but to request the amnesty laws from a willing Congress. Then, in 1990, then-President Carlos Menem took the controversial step of pardoning the military officers on the grounds of "national reconciliation."
Opponents charge that the two laws stifled further prosecutions as "Full Stop" put an end to any more trials of top officers while "Due Obedience" shielded lower-ranking officers from being charged with crimes on the grounds they were legally compelled to follow superior orders.
Kirchner has made human rights a priority of his fledgling administration, and his wife, Sen. Cristina Kirchner, made the final impassioned plea for scrapping the laws.
"The future (of the country) won't be built by sweeping all the dirt under the rug," she said, anger in her voice.
She said the two laws had put a grave chilling effect on attempts by the court to continue prosecuting dictatorship-era crimes.
"Parliament essentially told the judges that they could not try crimes like kidnapping and torture," said the president's wife.
But opponents charged that Congress was overstepping its authority by taking up a matter for the courts.
Lower courts have sporadically challenged the constitutionality of the amnesty laws since 2000, and ultimately, the Supreme Court is expected to be the final arbiter on their validity.
The push in Congress to overturn the amnesty laws gained new ground late last month after a federal judge detained dozens of former military officers from the dictatorship. Many of the 45 former officers are wanted in Spain in connection with the deaths or disappearances of its citizens in Argentina during the dictatorship.
Human rights groups are calling on Argentina to reopen investigations and extradite suspects for trial abroad. Yet opponents argue that new prosecutions would only reopen old wounds, foment fresh divisions and subject former officers to trials for crimes already pardoned.
By Debora Rey