In his 5 day pilgrimage to the nation, he prayed with victims urging them to overcome their grief by forgiving their assailants.
He also pressed the ex-fighters to have the boldness to request that forgiveness from their previous victims.
"As we look at it, we remember not only what happened on that day but also the immense suffering, the many deaths and broken lives and all the blood spilled in Colombia these past decades," Francis said.
He embraced both victims and perpetrators, saying families deserved to know the fates of missing relatives and children recruited to fight. However, he added that the truth should never lead to revenge.
Pope Francis had promised to visit the country after signing last year's peace deal with the Revolutionary Armed Forces of Colombia (FARC).
Before the event, the former rebel commander of the FARC published a public letter to Francis, asking for forgiveness.
Rodrigo Londono, better known by his nom de guerre Timochenko, is undergoing medical treatment in Cuba following a stroke and said he was unable to be present.
In another sign that the Pope's message of reconciliation may be getting through to the deeply polarised nation, the mayor of Medellin said President Juan Manuel Santos would pray on Saturday at a Mass in Colombia's second-largest city with his predecessor and arch-rival, Alvaro Uribe.
Previously the two had refused to appear together at any papal events.