Despite his insistence the trip would be "purely religious" he waded into the sensitive politics of the region, issuing a unique invitation to the Israeli and Palestinian presidents to pray with him at the Vatican to end their "increasingly unacceptable" conflict. Both accepted the invitation, although it was not clear when the visit would take place.
In a fitting gesture, Francis ended his visit by celebrating mass at the Upper Room on Mt Zion, where Jesus is believed to have held the Last Supper, where Christians have access but very limited freedom of worship. Vatican efforts to negotiate greater rights at the Upper Room have sparked opposition from nationalist and Orthodox Jews, who revere part of the building as the tomb of King David, prompting a series of angry protests and several anti-Christian attacks. Earlier, the pontiff had drive home a strong message about religious intolerance and called for "free access to holy sites" within Jerusalem. And he called for a "firm rejection" of intolerance towards "places of worship", in an apparent allusion to a wave of extremist hate crimes targeting mosques and churches.
On an early-morning tour of the holiest sites in Jerusalem's walled Old City, he issued a call for the three religions to "work together for justice and peace" as he was shown around the Al-Aqsa compound, the third holiest site in Islam. Entering the exquisite blue-tiled Dome of the Rock with its landmark golden cupola, used as a place of worship for women only, the pope first removed his shoes before walking down to visit the smaller, silver-domed Al-Aqsa mosque.
At the Western Wall, the holiest site at which Jews can pray, he left a note in between the ancient stones before sharing an emotional embrace with two close friends travelling with him, Rabbi Abraham Skorka and Islamic studies professor Omar Abboud.
Watching from a distance were a handful of ultra-Orthodox youngsters who shouted : "Tragedy, horrible!" in Yiddish. Francis had promised the three-day pilgrimage, which began on Saturday in Jordan, would steer clear of political issues. But at the end of an open-air mass in Bethlehem, where he began the Israel-Palestinian leg of his trip, he inviting Palestinian president Mahmud Abbas and his Israeli counterpart Shimon Peres to join him at the Vatican for a "heartfelt prayer" for peace. Peres told the pope he was happy to accept, while a senior Palestinian official confirmed Abbas would visit the Vatican for the prayer on June 6.