The pair, who have previously met several times, discussed peace efforts during a private half-hour audience according to the Vatican, which released images of them smiling together.
Abbas then met the Holy See's Secretary of State Cardinal Pietro Parolin and the Vatican's equivalent of a foreign minister, Paul Richard Gallagher.
The discussions focused on the Church's assistance in "the very serious humanitarian situation in Gaza", the hoped-for ceasefire, release of all hostages, and "achieving the two-state solution only through dialogue and diplomacy", a Vatican statement said.
The meeting comes a few days after the release of a photo showing Pope Francis praying in front of a nativity scene at the Vatican, where the baby Jesus's manger is covered with a black and white keffiyeh scarf, the symbol of Palestinian resistance.
The photo prompted a protest from the Israeli embassy to the Holy See, which asked for the keffiyeh to be removed, diplomatic and Vatican sources told AFP.
Francis has called for peace since Hamas's unprecedented attack against Israel on October 7, 2023, and the Israeli retaliatory campaign in Gaza.
In recent weeks he has hardened his remarks against the Israeli offensive.
At the end of November, he said that "the invader's arrogance... prevails over dialogue" in "Palestine", a rare position that contrasts with the tradition of neutrality of the Holy See.
In extracts from a forthcoming book published in November, he called for a "careful" study as to whether the situation in Gaza "corresponds to the technical definition" of genocide, an accusation firmly rejected by Israel.
Francis denounced an "immoral" use of force in Lebanon and Gaza at the end of September.
The Holy See has recognised the State of Palestine since 2013, with which it maintains diplomatic relations, and it supports the two-state solution.
Abbas is also due to meet Italian Prime Minister Giorgia Meloni and President Sergio Mattarella in Rome.
