Juan Manuel Santos went to the western town of Bojaya, where dozens of people had been left stranded by intense fighting between left-wing rebels and right-wing militias, and were killed in the place of worship 14 years ago.
Appearing visibly emotional, he said to residents: "You symbolise the suffering of the victims of 52 years of war and are at the centre of the solution to this conflict. The victims have taught me that the capacity to forgive can overcome hatred and rancour."
Mr Santos, who was awarded the Nobel Peace Prize on Friday, revealed he is donating his £750,000 award to victims of the conflict, through funding for infrastructure projects and victims groups.
He attended Mass in the church, where he was presented a replica of a statue of Jesus mutilated during the Bojaya massarce, which forms part of a war which has been raging since the mid-1960s.
A peace deal agreed by Mr Santos and the Revolutionary Armed Forces of Colombia (FARC) was narrowly rejected by voters in a shock referendum result, during the first weekend of October.
Meanwhile, demonstrators (pictured above) held hands in the Colombia capital, Bogota, on Saturday in support of the rejected peace agreement.
Bojaya has been visited on two occasions by FARC leaders, asking for forgiveness and discussing with community leaders how to help the rebuild following the deaths on 2nd May 2002.
Speaking in Bojaya, where 96 per cent of people supported the peace agreement, Mr Santos added: "I'm not going to falter a single minute. I'm not going to give up a single second" in searching for peace.