Addressing the nation, President Juan Manuel Santos said he accepted the result but would continue working to achieve peace.
The result of the referendum came as a shock to many. There could be several explanations for it:
- Low turnout
At under 40 percent, turnout was the lowest since the 1994 presidential election.
"Most Colombians who could have voted in this referendum did not chose to do so," Helen Yaffe, a Latin America specialist at the London School of Economics, told RFI.
"What's also very interesting as well is that, in the area the most affected by the war in Colombia, they tended to be overwhelmingly in favor to the 'yes' vote to the peace."
- Voters outside the conflict zone
But even with a low turnout, the 'yes' was expected to win. And the result was close, the difference is of less than 57,000 votes.
"The majority of the people who voted 'no' to the peace agreement do not live in conflict-afflicted areas in Colombia, they do not face the consequences," Kristian Herbolzheimer, a conflict resolution expert with Conciliation Resources, a UK-based peace consultancy, told RFI.
- Mistrust and resentment of Farc
"While Farc was never militarily defeated, in terms of propaganda, they were clearly defeated during the years of former president [Alvaro] Uribe, between 2002 and 2010," Herbolzheimer pointed out. "To the level that the vast majority of Colombians really don't trust Farc no matter what they do, no matter the gestures they have done these days and their request for forgiveness, that hasn't changed their mind. Farc lost the propaganda many years ago and they're now facing the consequences of that."
What happens next?
The signing parties say they want to continue working towards peace.
But there are several elements that the opposition, the 'no' camp, will probably never back down on.
"As far as any renegotiation goes, the main point, the crucial point, on the issues of justice and political participation are pretty much non-renegotiable," Philip Paterson, an Analyst on Latin America at Oxford Analytica, told RFI.
"The Farc leadership will never agree to go to jail and political participation is one of the key reasons for pursuing peace. So, sadly, at this stage, I don't see much being salvage from this."
It was never completely clear how much support for the peace process there was in Farc's ranks, either, he said.
"We already have one unit that said that it would not abide by the peace process, back in the summer, and I think that there's a good chance that other units will start to do the same now."
Could fighting resume?
As to whether fighting could resume - several opinions are emerging.
Oxford Analytica's Paterson believes it is quite likely that the fighting could resume.
On the other hand, Yaffe, at the LSE, says that inequality in land distribution and the defence of peasant communities, which are fundamental issues that led to Farc's formation, have not been resolved, for example.
Yet it is really hard to imagine that fighting will resume, she believes, especially after four years of peace talks, during which the Farc have not engaged in armed conflict and have maintained a bilateral ceasefire.
"It seems that both sides, have, since the referendum result, declared that they are committed to peace, the question now is what mechanism can they find to implement it, somehow bypassing the need for a national referendum," she said.
"Certainly, it's unlikely that Santos himself, who's based his presidency on this peace agreement, would allow it to fall by the wayside and I think that the Farc guerrillas can't really allow that either, they've already got rid of a significant mass of their armaments, so they're in a much more precarious situation now."
It is likely both sides will sit again at the same table to engage in further discussions but the war lasted so long that many Colombians may find it hard to ever forgive the Farc.