Wounded and bereaved civilians and former fighters exchanged words of forgiveness and wept as Francis urged the country to move on from Latin America's longest conflict.
"Throughout this long, difficult, but hopeful process of reconciliation, it is... Indispensable to come to terms with the truth," Francis said in the central town of Villavicencio.
"Truth is an inseparable companion of justice and mercy. Together, they are essential to building peace."
On the third day of his Colombian tour, Francis held a mass followed by a symbolically-charged ceremony of "prayer for national reconciliation."
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Pastora Mira Garcia spoke of how her father, husband and two children were killed by armed groups in the northwestern Antioquia region.
She recalled caring for a wounded paramilitary fighter who later admitted he was one of those who had tortured and killed her son.
"Now I place this pain and the suffering of thousands of Colombian victims at the feet of the crucified Christ, so that it may be transformed into a blessing and forgiveness to break the cycle of violence," she said.
Garcia told AFP afterward that she felt "totally reconciled and able to invite many other people to do the same."
Francis backed the contested peace process that has led to Colombia's biggest rebel group, the FARC, disarming and turning into a political party.
The government pushed the FARC accord through congress despite resistance from critics who said the rebels were getting off too lightly with amnesties and alternative sentences.
A separate official ceasefire has also been clinched with the last active guerrilla group, the ELN.
FARC leader Rodrigo Londono asked Francis in an open letter Thursday for his "forgiveness for any grief or pain we have caused to the people of Colombia."
At the prayer ceremony, Juan Carlos Murcia, 38, told of his 12 years in the FARC after being recruited as a 16-year- old boy.
He lost his left hand while handling explosives. He now runs a sporting foundation to keep young people away from drugs and violence.
"I ask for forgiveness if at any time I caused pain to a family or a person," he said in an interview.
On a wall during the reconciliation prayers hung a mutilated Christ effigy that was all but destroyed by a deadly FARC bombing in the western town of Bojaya in 2002.
During the ceremony, Luz Dary Landazury recalled nearly losing a leg from a landmine laid by guerrillas.
She now works to protect people from landmines left over from the conflict.
She left one of her crutches as an offering to the Bojaya Christ.
Pope Francis was joined in the mass by leaders from indigenous communities stricken by the conflict.
At the morning mass, Jesus Mario Corrales, 52, said he was dislodged from his land by the FARC in the late 1990s and later also abused by paramilitaries.
The Colombian conflict has left 260,000 people confirmed dead, 60,000 unaccounted for and seven million displaced.
"Besides forgiveness, I want them to return the bones... so we can pray for our relatives," Corrales said.
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