Speaking to Vatican foreign affairs official Dominique Mamberti after the talks, he said: "It was a pleasure and I invited him to the Holy Land".
Abbas gave the pope a ceramic panel with a view of Bethlehem and a Bible as gifts, while Francis gave him a decorative pen with which Abbas said he hoped to sign a peace agreement with Israel.
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"Soon, soon," the pope responded.
Israeli President Shimon Peres also invited Francis during a visit earlier this year and Israeli Prime Minister Benjamin Netanyahu is due to be received by the pope on Wednesday next week.
Francis has already said he would like to travel to the Middle East but the Vatican has not confirmed the trip, despite a report by Israel's Channel 2 television that it will take place in March.
Francis has said he would like to visit with patriarch of Constantinople Bartholomew I, the spiritual leader of the world's Orthodox Christians.
Abbas is the fourth Middle East leader to meet Pope Francis after Peres, Lebanese President Michel Sleiman and King Abdullah of Jordan.