The pontiff invited President Juan Manuel Santos and his right-wing rival, former President Alvaro Uribe, to discuss the country's peace accord with rebels.
The Vatican has released pictures of the trio talking together in the Pope's office. President Santos presented the Pope with a pen made out of a bullet used in the civil war that was engraved with the words "The bullets have written our past, education will write our future".
Uribe led the campaign against Santos's deal with the Revolutionary Armed Forces of Colombia that resulted in a shock rejection by Colombians in an October referendum.
Santos then introduced several changes to the deal to appease his critics and signed the deal with the rebels on 25 November despite the referendum outcome.
President Santos received the Nobel Peace Prize this year for his efforts to end the longest running conflict in the region.