Santos was awarded the Nobel Peace Prize later in October despite that outcome in a move that many believe was meant to put pressure on Santos and his political rival, former President Álvaro Uribe.
Rather than risk rejection in another referendum, Santos, who won the 2016 Nobel Peace Prize, chose to submit the revised accord to the Congress for approval.
The years of violence has left 260,000 people dead and 60,000 missing. The treaty was to end all armed conflicts in Colombia; fighting that had spanned the nation since 1964.
After marathon debate sessions, Colombia's Senate ratified the deal Tuesday followed by the House late Wednesday.
Santos says ratification will set in motion the start of a six-month process in which the FARC's 8,000-plus guerrillas will concentrate in some 20 rural areas and turn over their weapons to United Nations monitors. "This last part of renegotiation was exhausting", said governmental peace official Sergio Jaramillo to the press after the House vote.
The legislative approval was a final victory for Santos and FARC leader Rodrigo Londono, who signed the original peace accord in September after almost four years of talks only to have it narrowly rejected by Colombians in a nationwide referendum.
The first peace accord, reached after four years of talks, was narrowly rejected in a referendum in October.
Colombia's congress passes historic peace deal with guerrillas, but battles remain
"We incorporated the greatest possible number of changes in this exhaustive work", said Humberto de la Calle, the government's chief negotiator, in a statement.
They range from a prohibition on foreign magistrates judging crimes by the FARC or government, to a commitment from the armed fighters to forfeit assets, some of them amassed through drug trafficking, to help compensate their victims.
Days after the agreement's stunning rejection by Colombia's voters, Santos was awarded the Nobel Peace Prize for his efforts to end the war.
Sergio Jaramillo, the High Commissioner for Peace said, "We can not forget what we are doing".
Mr Uribe's supporters argued the deal offered too many concessions to the FARC and did not serve as a deterrent for other groups involved in crime.
The revised deal does not need to be approved by voters.
The government of Juan Manuel Santos announced Wednesday that after canceling talks with the country's second-largest guerrilla, the ELN, they will now go ahead in January 2017. The half-century war between the FARC and the Colombian government claimed the lives of a quarter of a million people.