President Juan Manuel Santos and guerrilla leader Rodrigo "Timochenko" Londono signed the new deal with a pen made from a spent bullet, in a low-key ceremony in the capital Bogota.
The original deal -- signed with great fanfare in September -- was rejected by voters in a referendum last month, a shock upset that sent negotiators back to the drawing board.
The new plan bypasses a vote by the Colombian people, against bitter opposition from critics.
Santos, who won this year's Nobel Peace Prize for his efforts to end the conflict, said the new deal was better than the original.
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"It includes the hopes and observations of the vast majority of Colombians," he said after signing it.
"We all know in our souls that the cost of the armed conflict is too high."
The deal was immediately sent to Congress, where it is expected to pass after being debated next week. Santos and his allies hold a majority in the legislature.
A recent wave of alleged assassinations in conflict zones has added to calls to seal a deal fast.
But an aftermath of discord and uncertainty appears likely as opponents promised to keep resisting the peace plan, including with street protests.
"The country has spoken. It has said, 'Yes to peace, but without impunity,'" said top opponent Alvaro Uribe, a conservative ex-president and senator.
"What we have here remains total impunity," he told RCN television.
Speaking later in the Senate, he called for another referendum on some of the contested "basic issues" in the deal.
But Uribe complains it still ignores key demands, notably on punishing FARC leaders for the killings and kidnappings blamed on the group.