Santos is awarded for his resolute efforts to bring the country's more than 50-year-long civil war to an end, a war that has cost the lives of at least 220 000 Colombians and displaced close to 6 million people.
The award came despite voters' shock rejection of the terms of a historic deal he reached in September with FARC chief Rodrigo Londono, alias Timoleon "Timochenko" Jimenez, after nearly four years of talks.
Santos is the 15th Head of State or Government at the time of the award.
"The Norwegian Nobel Committee has decided to award the Nobel Peace Prize for 2016 to Colombian President Juan Manuel Santos for his resolute efforts to bring the country's more than 50-year-long civil war to an end," said committee chairwoman Kaci Kullmann Five.
The announcement caught most Nobel watchers off-guard, with most experts saying that the referendum had torpedoed Colombia's chances of winning.
The Norwegian Nobel Committee said the aim was to encourage peace efforts in the war-torn country, which are now in "real danger" of collapse.
"We hope that it will encourage all good initiatives and all the parties who could make a difference in the peace process and give Colombia -- finally -- a peace after decades of war," Kullman Five said.
The Colombia conflict has killed more than 260,000 people and left 45,000 missing over five decades, drawing in several leftist guerrilla groups, right-wing paramilitaries and drug gangs.
Under the terms of the deal, FARC, the oldest and largest rebel group, was to relaunch as a political party.
Asked why the prize had not been jointly awarded to the FARC leader, Kullman Five declined to answer, saying: "We will never comment on other candidates and other possibilities."
The committee said the award was also "a tribute to the Colombian people" who had not given up hope of a just peace as well as to the families of the "countless victims" of the war.
The people's rejection of the terms of the deal followed a successful campaign by rightwing hardliners angered by the offer of impunity for the Marxist rebels.
And with the ceasefire due to expire at the end of October, the country is now teetering on the brink -- of either war or peace.
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