And while a meeting of the deal's principals is scheduled for Monday morning, FARC's financial disclosures -- and possibly a disarmament campaign that began last week-- have been questioned.
In the weeks leading up to Sunday's vote, many Colombians were angered by what they saw as insufficient punishment for those who perpetrated a litany of crimes against their people.
It's estimated 220,000 were killed in the 52-year conflict which displaced as many as 5 million people.
At the height of its terror campaign, the armed group seized territory, attacked government forces and conducted high-profile kidnappings. The rebels also hijacked planes, made millions trafficking cocaine and forced children to fight.
For just over half of those who voted, the FARC's past crimes were too much to forgive.
Was there a plan B?
The rejection of the plan has left the administration of President Juan Manuel Santos wrongfooted and, as the president himself said, "without a plan B."
Now the rebels and the Colombian government, facilitated by international leaders, will have to go back to the drawing board to re-imagine a peace that is acceptable to the people of Colombia, speaking on behalf of the victims of murder, extortion and kidnapping.
"I hear those that said 'no' and those that said 'yes' and we all want peace. Tomorrow we will get all our political parties together to continue dialogues and finding alternatives for peace. I will not give up, I will continue to fight for peace," Santos said.
What happens now?
It is largely unclear what the path forward looks like. Santos said Sunday a ceasefire will remain in place and negotiations will continue in Havana, Cuba, while his counterpart, FARC leader Rodrigo Londoño Echeverri, agreed that the referendum result would not sway the former rebels from the path of peace.
"With today's result, we know that our challenge as a political movement is even greater and demands for us to be stronger, to build up a durable and stable peace," Londoño, who also goes by the alias Timoleón "Timochenko" Jiménez, said Sunday night.
"The FARC-EP maintains the willingness for peace and they reaffirm their disposition to use only the word as a constructive weapon towards the future. To the Colombian people who dream with peace, they can count on us. Peace will triumph."
Can a new deal be agreed?
The country is divided, says Virginia Bouvier, Senior Advisor for Latin American Programs at the US Institute of Peace, and while the accord represented a "unique and very exciting endeavor to hold accountable those who have committed horrific crimes," opponents of the deal reduced it to an oversimplified outcome: whether former rebels would see the inside of a jail cell.
Regardless of the outcome, "the path of peace will continue and both sides will follow it," Bouvier told CNN via Skype.
"Santos... speaking as president of all those who voted, said that he recognized that he had put it to a vote but maintained that he would be convening all political sectors to enter in dialogue and take that back to Havana.
"Trying to implement something that half of the population is against it is very difficult," she said, adding that in Colombia today there are deep divisions and the country polarized.
"I think this gives an option to go back to the drawing board to tweak to see what works for the entire population. I wish the (dealmakers) tremendous stamina for the next stage," she said.
Will there be political repercussions?
Almost without doubt. The 'no' vote was seen as somewhat of a referendum on Santos, who lost support through his agreement to sit down with the rebels.
The 'no' campaign was led by his predecessor, Álvaro Uribe, who would like to run again as president.
"This is a huge blow to the political future of President Santos," Journalist Simone Bruno told CNN.
"Just a few days ago we saw him signing this important agreement with the FARC leader and had huge support from the international community.
"He was one of the main candidates for the Nobel Prize and now he has to go back again. What he said is that he will never lose the chance to negotiate until the last day of his mandate. Now he wants to keep on going, keep on negotiating but of course of things are changing and nobody really knows what will happen tomorrow."
What could a new deal look like?
It's unlikely that the FARC leadership would give up former rebels to jail time to satisfy the demands of the slim majority which rejected the deal. FARC members and supporters already feel that the group has conceded too much in its quest for a settlement.
Santos has called a meeting of the principals of the imperiled deal for Monday morning in Bogota to decide what step to next take. One thing is for sure; no one wants a return to all-out conflict between government troops and a dwindling band of rebels in Colombia's jungles.
As so little is known about what comes next, it is unclear if the process to get the derailed deal back on track will happen quickly or slowly. The president still holds a majority in congress and will do so for the two remaining years of his term, so while the vote result is politically damaging he still has a lot of sway in congress.
It is unlikely that the whole deal will be scrapped, but rather the contentious clause which keeps former rebels out of jail will be renegotiated.