Pope Francis on Monday made an impromptu stop at an Israeli memorial for victims of militant attacks, on the final day of his whirlwind Middle Eastern pilgrimage.

The unscheduled gesture, which came as he visited the national cemetery on Mount Herzl, reportedly took place at the personal request of Israeli Prime Minister Benjamin Netanyahu, army radio reported.

It comes a day after the 77-year-old Argentine made another surprise stop to briefly pray at Israel's West Bank security barrier in Bethlehem, in a gesture the Palestinians hailed as an "eloquent and clear message".

The pontiff was on Monday rounding off a whirlwind trip which saw him issue a unique invitation to the Israeli and Palestinian presidents to pray with him at the Vatican to end their "increasingly unacceptable" conflict.

On an early-morning tour of Jerusalem's walled Old City, Francis called for Christians, Jews and Muslims to "work together for justice and peace" as he was shown around the Al-Aqsa compound, the third holiest site in Islam which Jews also consider sacred.

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 prayed for a few moments and left a note in between the ancient stones before sharing an emotional embrace with two close Jewish and Muslim friends travelling with him.

Francis had promised the three-day pilgrimage, which began on Saturday in Jordan, would steer clear of political issues.

But he ad-libbed from a scripted speech to condemn anti-Semitism, religious intolerance and those behind conflicts in the Middle East.

During the morning, he also visited the Yad Vashem Holocaust memorial, where he denounced the "abyss" of the Nazi genocide which claimed the lives of six million Jews.

Speaking at the Hall of Remembrance, long, dark stone room with the names of the Nazi death camps inscribed on a granite slab, Francis spoke of "the boundless tragedy of the Holocaust" describing it as an "unfathomable abyss".

And later, on meeting Israel's two chief rabbis, Francis expressed hope that Jews, particularly "young people", would demonstrate a "growing interest in knowledge of Christianity".

As a gift, the two rabbis gave him a replica of a fragment of the ancient Dead Sea Scrolls on which was written the Ten commandments.