The pontiff was speaking as the end of the talks which took four years of negotiating.
The conflict began in the 1960's between the opposing factions and almost a quarter of a million people have been killed to date.
There are an estimated eight million victims and the country has the world's largest number of internally displaced people, 6.9 million.
A statement from the Vatican said the pope "reiterates his support for the goal of attaining the peace and reconciliation of the entire Colombian people, in light of human rights and Christian values, which are at the heart of Latin American culture."
It went on to say: "Pope Francis commends the peace process in Colombia to the maternal protection of the Most Holy Mother of God, Queen of Peace, and he invokes the gift of the Holy Spirit to enlighten the hearts and minds of those who are called to promote the common good of the Colombian nation."
The people of Colombia will vote on the peace deal on 2nd October according to President Juan Manuel Santos.
