After nearly eight hours of debate and a week after the country's lower house had also voted for the move, the Senate approved the annulment of the laws passed in the mid-eighties.
A majority of the Senate's 51 members voted in favour of the measure abolishing the laws, said Senate president Jose Luis Gioja, without providing the exact vote count.
The laws passed a few years after the end of the 1976-1983 military dictatorship, barred prosecution of military leaders for human rights violations.
The abolition of those laws is expected to be signed into law by President Nestor Kirchner, who has launched a crackdown on impunity to shore up public trust in the government.
The Senators also ratified a Chamber of Deputies decision to sign the 1968 Convention on the Non-Applicability of Statutes of Limitations to War Crimes and Crimes Against Humanity.
The passage of the two measures open the door for charges to be brought against hundreds of members of Argentina's security forces, accused of human rights violations.
The amnesty laws prohibiting their prosecution were passed by the government of ex-President Raul Alfonsin and were followed by pardons granted by his successor, Carlos Menem.
An estimated 15,000 to 30,000 people, mostly opponents of the military regime, were killed during the dictatorship.
The majority were kidnapped and their bodies never recovered.