The pontiff told people to instead arm themselves with peace and forgiveness.
He issued the appeal from the altar of Bangui's cathedral after arriving in the badly-divided capital on the final leg of his three-nation African tour.
"My wish for you, and for all Central Africans, is peace," Francis told the nearly 4,000 residents in the St Sauveur church camp.
With the help of a Sango translator, he then led them in a chant: "We are all brothers. We are all brothers."
"And because we are brothers, we want peace," he said.
Sunday's visit was a moment in history for the Central African Republic, where Muslim rebels overthrew the Christian president in early 2013.
Since then a conflict has been ongoing between the faiths.
Overall, one million people in a country of 4.8 million have been forced from their homes.
Francis plans to enter this highly volatile neighbourhood on Monday morning to meet with the local imam and Muslims in the mosque before returning to Rome.
He also reminded the faithful that their primary role was to love their enemy and be courageous in forgiving and overcoming hatred, violence, persecution and injustice: "To all those who unjustly use weapons in this world, I appeal: Put down your weapons of death; arm yourselves instead with justice, love, mercy and authentic guarantees of peace," he said to applause.
The Muslim community, as well, hopes the visit will improve the bleak condition people are living in.
Adoum Silick, 45, admitted there was risk in going to the grounds of the cathedral but said "sometimes we have to be courageous."
"Life is very difficult for the Muslims who remain.
"I am taking advantage of all the security here to come."
"The pope is a great mediator and we must listen to his message."
