He will meet senior Israeli and Palestinian leaders, top Christian, Jewish and Muslim religious officials, and Palestinian refugees living in the shadow of Israel's controversial separation barrier near the spot where Jesus is believed to have been born in Bethlehem.
His trip is a mainly pastoral visit aimed at encouraging the dwindling Christian population to stay in the Holy Land, as well as promoting peace and inter-faith dialogue in a conflict-ridden region sacred to the world's three main monotheistic religions.
On arrival in Jordan on Friday, the pontiff said he came "as a pilgrim, to venerate holy places," adding that the Church "is not a political force but a spiritual force which can contribute to the progress of the peace process" in the Middle East.
Security-obsessed Israel is rolling out stringent measures for the trip, with tens of thousands of law enforcement officers deployed, entire sections of Jerusalem to be shut down at various times and Israeli air space to be closed for the papal arrival as part of "Operation White Robe."
Israel-Vatican relations were strained by Benedict backing the beatification of his controversial Nazi-era predecessor Pius XII and lifting the excommunication of a Holocaust-denying British bishop.
Speaking on Saturday on the slopes of the windswept Mount Nebo, where biblical tradition says God showed Moses the Promised Land, Benedict called for reconciliation between Christians and Jews, calling the bond between the Church and the Jewish people "inseparable."
Among his first stops in Israel will be the Yad Vashem Holocaust Memorial, where he will lay a wreath in memory of the six million Jews killed by the Nazis.
But he will shun the part where a caption under the photo of Pius XII says the war-time pope failed to protest against the Holocaust -- a stance that has angered the Vatican which disputes the claim.
Ahead of Benedict's arrival, Yad Vashem said that relations with the Vatican would improve if evidence emerges that Pius XII helped the Jews.
Israel has pumped some 10 million dollars (7.5 million euros) into preparations for the visit, but the unbridled enthusiasm that greeted Pope John Paul II's historic trip in 2000 -- the first by a pontiff since Israel and the Vatican established diplomatic ties in 1993 -- is missing this time around.
Benedict unleashed a torrent of criticism in January when he lifted the excommunication of British bishop Richard Williamson and three other ultra-conservative bishops in what he called a "discreet gesture of mercy."
Coupled with the Pius beatification and with Benedict's membership of the Hitler Youth -- he has said he was enrolled against his will after membership became compulsory in 1941 -- these incidents have created concern in the Jewish community.
"People are suspicious of his motives. They think he's hardline... conservative," said Yaacov Katz, a professor at Bar-Ilan University.
But Rabbi David Rosen, chairman of the International Jewish Committee on Inter-religious Consultations, said that such unease is unjustified.
"Catholic-Jewish relations are extremely warm right now and probably never been as good as they are."
Over the past several months, hectic preparations have gone on ahead of the visit.
In Nazareth, dozens of earthmovers have been tearing up a flank of Mount Precipice where the pope will give a mass.
In the Church of the Holy Sepulchre in Jerusalem's Old City, the Franciscan monks closed down their chapel for a week to paint the peeling ceiling.
"He won't be looking up but we'll be looking up and cringing," Father Fergus Clarke, the head monk, said ahead of the works.
In the Aida refugee camp at the gates of Bethlehem, residents hope to use the visit to attract the world's attention to Israel's controversial eight-metre (25-foot) high concrete wall towering above much of the city.
"Welcome Pope in Aida Camp," someone painted in English on the imposing structure.