Both leaders accepted the pope's invitation, which comes after U.S.-mediated Mideast peace talks broke down in April.
Vatican spokesman Federico Lombardi explained that Pope Francis' offer to bring the two leaders together in Rome is intended to help "build peace within the perspective of prayer."
At his meeting with Palestinian authorities in Bethlehem, the pope declared that "The time has come for everyone to find the courage...to forge a peace that rests on the acknowledgment by all of the right of two states to exist and to live in peace and security within internationally recognized borders."
Pope Francis also made a point to stop at the Israeli wall separating Jerusalem from Bethlehem on Sunday. The impromptu visit to the wall, where the pope prayed silently, was considered "courageous" by former Palestinian peace negotiator Ghassan Khatib.
The pope was expected to travel to Tel Aviv late Sunday for meetings with President Peres and Prime Minister Benjamin Netanyahu.