The 80-year-old Argentine pontiff spoke alongside Colombia's President Juan Manuel Santos, who has overseen recent controversial efforts to make peace with armed rebel groups.
"The steps taken give rise to hope, in the conviction that seeking peace is an open-ended endeavour, a task which does not relent, which demands the commitment of everyone," Francis said.
"May this determination help us flee from the temptation to vengeance and the satisfaction of short-term partisan interests."
Francis arrived in Colombia on Wednesday for a five-day tour on which he will meet people bereaved and wounded in the conflict.
But the peace process has been fraught with division.
Critics of the accord with the FARC say the rebels got off too lightly, with amnesties and alternative sentences.
The FARC has transformed into a political party.
Colombians narrowly rejected the FARC peace deal in a referendum last year.
Francis tried unsuccessfully to mediate between Santos and the lead opponent of the accord, conservative leader Alvaro Uribe.
A reworked version of the accord was later pushed through Congress despite Uribe's resistance.
At his open-air encounter with Santos in front of the presidential palace, Francis hugged local children dressed all in white as a choir sang a song of peace.
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