Among the youth he met was Emmanuel, son of Clara Rojas, an MP today who was taken hostage in 2002 and held by the FARC for years in the jungle, where the boy was born.
Santos, who has promoted the peace accord in the face of stiff opposition, called the Pope's visit a "push" to take the first steps toward peace and reconciliation.
On his drive to the Vatican Embassy in central Bogota, the leader of the world's Roman Catholics was mobbed in the "popemobile" by screaming crowds tossing flowers and holding up children to be kissed.
"It's not the law of the most powerful, but rather the power of the law, approved by all, that regulates peaceful coexistence", Francis said, adding that just as laws are needed that can ensure harmony and help overcome conflicts, there also are laws required not because they respond to a pragmatic need to order society.
President Juan Manuel Santos, who won a Nobel Peace Prize in 2016 for his reconciliation efforts, told Italy's Il Messaggero newspaper that the visit would "motivate [Colombians] to continue on the path of reconciliation".
"This is the peace we are constructing", he told the Pope. "A stable and lasting peace, so that we can see one another and treat one another as brothers, not as enemies". Francis was cheered on by an estimated 700,000 people who had waited many hours to welcome this "messenger of peace and reconciliation" to a deeply polarized nation.
"We do not want any type of violence whatsoever to restrict or destroy one more life", he said.
"I'm convinced that the only way out of the conflict is dialogue", said Dairo Usuga, appearing publicly for the first time, in a video published on social media.
Pope Francis will travel to three other cities, where he will meet victims of the country's civil war.
The pope then turned his attention to Venezuela where, he said, "may dialogue happen and may the country rediscover a good stability with the dialogue of all".
And the meeting will be framed by one of the most poignant symbols of the conflict: a mutilated Christ statue that was rescued from a church in the western town of Bojaya after a FARC mortar attack in 2012.
Ahead of Francis' arrival, Santos' government and the last remaining major rebel group, the National Liberation Army, or ELN, signed a bilateral cease-fire agreement, a significant step toward negotiating a permanent peace deal. At least four people have been taken away in stretchers.
The violence has left 260,000 people confirmed dead, 60,000 unaccounted for and seven million displaced.
The Vatican No. 2, Cardinal Pietro Parolin, said the key message of the trip is "the capacity to forgive: to forgive, and receive forgiveness".
"We trust your visit will open the hearts and minds of Colombians to the peace that comes from God and inhabits the souls of men". Both used their visits to show solidarity with victims of violence, discrimination and poverty and to urge government authorities to fix the structural and societal problems that have made Colombia one of the most unequal countries in Latin America.