President Juan Manuel Santos said on Twitter: "Thanks to the Congress which in a historic vote approved the amnesty law, first step toward consolidating peace."
The measure grants special legal treatment, amnesty and pardon to members of the Revolutionary Armed Forces of Colombia (FARC) accused of political and related crimes.
The Senate passed the bill 69-0, after the House of Representatives approved it 121-0.
The amnesty bill is part of the November 24 pact aimed at ending five decades of conflict.
Former president Alvaro Uribe spearheaded opposition to the peace deal after nearly four years of negotiations to end more than half a century of armed conflict.
The former president and his allies argue the deal grants impunity to rebels guilty of war crimes, giving them seats in Congress rather than sending them to prison.
After voters rejected the earlier deal by a narrow margin, the government and the FARC renegotiated it, deciding to have it ratified in Congress rather than risk a second referendum.
The conflict has killed more than 260,000 people and left 45,000 missing.
