But it needed to be ratified by Colombians in order to come into force. Addressing the nation, President Santos said he accepted the result but would continue working to achieve peace.
He said the current ceasefire remained in place and that he had ordered negotiators to travel to Cuba to consult Farc leaders on the next move.
"I won`t give up," he said. "I`ll continue the search for peace until the last moment of my mandate because that`s the way to leave a better country to our children."
Meanwhile the Farc leader, known as Timochenko, said the group remained committed to securing an end to the war.
The rebels earlier agreed to lay down their weapons after 52 years of conflict to join the political process. But critics said the deal treated the Farc, which the US still considers a terrorist group, too leniently.
The agreement was rejected with 50.2% of voters against it and 49.8% in favour - a difference of less than 63,000 votes out of 13 million ballots.
The surprise result means the peace process is now shrouded by uncertainty.
Former President Alvaro Uribe, who headed the "no" campaign, said all Colombians wanted peace, but that the deal needed "corrections".
"We want to contribute to a national accord and be heard," he said.
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