He called for a "just and lasting solution" so that Israelis and Palestinians may live in peace. He said Israel deserves peace and security "within internationally recognized borders," while the Palestinians have a "right to live with dignity and with freedom of movement" in their own homeland.
He also condemned the Holocaust as the "enduring symbol of the depths to which human evil can sink." Francis is to visit Israel's national Holocaust memorial, Yad Vashem, on Monday.
Veering off a prepared text, Francis deplored "this criminal act of anti-Semitic hatred" in Brussels, where three people, including two Israelis, were killed in Saturday's museum shooting.
"With a deeply pained heart, I think of those who have lost their lives in the cruel attack that occurred yesterday in Brussels," he said. "I entrust the victims to God's mercy and invoke recovery for the injured."
Earlier, Israel's president, Shimon Peres, thanked Francis for his strong stand against anti-Semitism and noted the timing of the Brussels shooting.
"You carry a message of brotherhood among peoples, and friendship for all," Peres said.
Francis arrived from the West Bank town of Bethlehem, where earlier Sunday he voiced strong sympathy for the Palestinians.
During his trip to the cradle of Christianity, France plunged into Mideast politics, calling the current stalemate in peace efforts "unacceptable" and winning the acceptance from the Israeli and Palestinian presidents to pay a symbolic visit to the Vatican next month to pray for peace.
In another unscripted moment, he prayed at the Israeli separation barrier surrounding the biblical West Bank town and briefly donned the checkered black and white headscarf that is a symbol of the Palestinian cause.