The unscheduled stop came after he called for an end to the “increasingly unacceptable” Palestinian-Israeli conflict.
Speaking in Bethlehem, Pope Francis invited the Israeli and Palestinian presidents to the Vatican to pray for peace.
The tour’s official purpose is to improve ties with the Orthodox Church.
Pope Francis is to meet Bartholomew I, the Orthodox Patriarch of Constantinople, in Jerusalem later – to commemorate the 50th anniversary of a historic meeting of Catholic and Orthodox leaders who moved to end 900 years of division between the two churches.
The Pope’s visit comes just weeks after peace talks between Israel and the Palestinians broke down, and his invitation to Rome for Presidents Peres and Abbas – quickly welcomed by both – is an intriguing development.
Following the Mass in Bethlehem, Pope Francis flew by helicopter to Tel Aviv where he was formally welcomed to Israel by President Shimon Peres and PM Benjamin Netanyahu.
“The time has come to put an end to this situation which has become increasingly unacceptable,” the Pope said on Sunday as he met Palestinian leader Mahmoud Abbas.
Pope Francis talked of the “tragic consequences of the protracted conflict” and the need “to intensify efforts and initiatives” to create a stable peace – based on a two-state solution.
He later held an open-air Mass for 8,000 local Christians by Bethlehem’s Church of the Nativity, during which he said he wished to invite Mahmoud Abbas and Shimon Peres to join him at the Vatican “in heartfelt prayer to God for the gift of peace”.
According to Pope Francis’ spokesman, Federico Lombardi, the move was papal peace initiative and believed to be the first of its kind.
Pope Francis has insisted the purpose of his Middle East trip is purely religious, but his first speech on his arrival in Bethlehem showed he is also willing to address pressing political issues, correspondents say.
On his way to Bethlehem, Pope Francis stopped to pray at an 8 m concrete wall that is part of the barrier Israel is building in and around the West Bank.
The Pope rested his head against the wall – which Israel says is needed for security, but the Palestinians see as a land grab – near graffiti reading: “Free Palestine.”
Palestinian officials have noted that Pope Francis is the first pontiff to travel directly to the West Bank rather than enter via Israel: Many Palestinians see that as a recognition of their push for full statehood.
The Pope’s tour began on Saturday with a visit to Jordan.
On Monday Pope Francis is due to visit the al-Aqsa mosque complex in Jerusalem’s Old City followed by the Dome of the Rock and the Western Wall.
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