"I make this appeal to the many young people throughout the Palestinian territories today," he said.
"Do not allow the loss of life and the destruction that you have witnessed to arouse bitterness or resentment in your hearts."
However, Nour Odeh, Al Jazeera's correspondent reporting from Bethlehem, said that many Palestinians had hoped for a stronger statement from the pope.
"A lot of hope rests on this visit and the moral authority the pope commands around the world," she said.
"People were probably expecting something clearer, something stronger on the political aspirations of the Palestinians and their rights to keep their land and live in that land with free access to their holy sites and the ability to develop and prosper like other populations."
Ismail Haniya, the Palestinian leader of the political faction Hamas, had called on the pope to visit Gaza to see what he described as "the real holocaust against the Palestinian people".
In 2008, Israel launched a three-week assault on the occupied Gaza Strip, killing more than 1,300 people and destroying much of the impoverished area's infrastructure.
Gaza is not on the itinerary for the pope's week-long pilgrimage, which has already taken in holy sites in Jordan and Israel.
As Abbas welcomed the pope to Bethlehem, he also condemned the Israeli occupation.
"In this holy land there are those who continue to build separation walls instead of bridges and see,k by the forces of the occupation, to compel Muslims and Christians to leave the country," he said.
|Palestinian nuns gather for mass in Manger Square [Reuters]
Abbas criticized Israel's West Bank separation wall, which nearly encircles Bethlehem.
"Your holiness is fully aware of the situation in Jerusalem which is surrounded by an apartheid wall which forbids our people in the West Bank from reaching the Church of the Holy Sepulchre and the Al-Aqsa mosque," Abbas said.
The pope was scheduled to visit an altar directly adjacent to the seperation wall that had been built in anticipation of his arrival. But the Vatican changed plans at the last minute to avoid controversy as Israel has asked that the altar be demolished.
Instead, the pope will visit a UN-run school opposite the wall. The pope passed through the wall on his way into Bethlehem.
"He saw for himself firsthand what the wall means and what impact it can and does have for on the Palestinians in Jerusalem and Bethlehem," Odeh reported.
"Many believe just that experience would lead the pope to have a very a strong statement on the wall, that it must be torn down as his predecessor John Paul II had advocated and as international law states."
At an open-air mass, the pope appeared to refer to the wall when he called for "greater freedom of movement, especially with regard to contact between family members and access to holy places."
While the Christian population of Bethlehem and Palestinian territories in general have decreased significantly in recent years, some hope the pope's visit will prevent Christians from leaving the Holy Land.
Earlier during his trip, while in the Josaphat Valley, the pope said it was a "tragic reality" that so many Christians had left.
"In the Holy Land there is room for everyone," he said.