"The award should also be seen as a tribute to the Colombian people who, despite great hardships and abuses, have not given up hope of a just peace, and to all the parties who have contributed to the peace process," Kaci Kullman Five added.
Juan Manuel Santos
Born in Bogota in 10 August 1951 in an influential family
Elected Colombian president in 2010 and re-elected in 2014
Served as defence minister from 2006 until 2009
Married, has two sons and one daughter
Sources: BBC Monitoring, Colombian presidency
Mr Santos said on Twitter: "This honourable distinction is not for me, it's for all the victims of the conflict. Together we'll win the most important award of them all: peace."
The peace deal was rejected by 50.2% of voters who went to the polls on 2 October.
The committee acknowledged the result, saying: "What the 'No' side rejected was not the desire for peace, but a specific peace agreement."
It also said that finding a balance between the need for reconciliation and ensuring justice for the victims would be a difficult challenge.
Also on Twitter, Farc leader Timochenko said: "I congratulate President Juan Manuel Santos, Cuba and Norway, who sponsored the process, and Venezuela and Chile, who assisted it, without them, peace would be impossible."
Earlier, he had written: "The only prize we aspire to is peace with social justice for Colombia, without (right-wing) paramilitary groups, without retaliation or lies. Peace in the streets."
A deal that wasn't: By Jonathan Marcus, BBC diplomatic correspondent
This was a Peace Prize for a peace deal that wasn't. President Santos joins a long line of Nobel Peace Prize winners who have been rewarded for effort as much as achievement.
But it is too easy to be cynical. The Nobel Peace Prize has often been controversial. In recent years a variety of international bureaucracies have won - the EU, the IAEA and the OPCW.
Why, some have argued, should people get a prize for simply doing their job? What, others ask, had US President Barack Obama actually done to merit the prize in 2009, other than be elected?
But the Nobel has often gone to extraordinary individuals who really have gone above and beyond to bring peace - in Northern Ireland and East Timor to name just two examples. Maybe the award to President Santos may yet galvanise public opinion in Colombia to think again about the deal.
Critics, led by former president Alvaro Uribe, said the deal was too lenient to the rebels.
Under the agreement, special courts would have been created to try crimes committed during the conflict.
Those who confessed would have received lighter sentences and avoided serving any time in conventional prisons.
The Farc would also have been guaranteed 10 seats in the Colombian Congress in the 2018 and 2022 elections.