The pope spoke from Mount Nebo, the hill overlooking the Jordan Valley from where the Bible says Moses saw the Promised Land.
The pope arrived at the site on the second day of a weeklong visit to the Middle East that will also take him to Israel and the Palestinian territories.
"May our encounter today inspire in us a renewed love for the canon of sacred scripture and a desire to overcome all obstacles to the reconciliation of Christians and Jews in mutual respect and cooperation in the service of that peace to which the word of God calls us," said Benedict.
The pope sparked outrage among many Jews earlier this year when he revoked the excommunication of an ultraconservative bishop who denies the Holocaust.
Benedict had lifted his excommunication along with three other ultraconservative prelates in a bid to end a church schism. But amid the uproar, the church has not allowed the bishop to resume his duties.
The pope's forceful condemnation of anti-Semitism and acknowledgment of Vatican mistakes have softened Jewish anger over the bishop. But another sore point has been World War II Pope Pius XII, whom Benedict has called a great churchman. Jews and others say he failed to do all he could to stop the extermination of European Jews.
The pope's visit to Mount Nebo was the first of many that Benedict will make to holy places during his first visit to the Middle East.
"The ancient tradition of pilgrimage to the holy places also reminds us of the inseparable bond between the church and the Jewish people," said Benedict. "From the beginning, the church in these lands has commemorated in her liturgy the great figures of the patriarchs and prophets, as a sign of her profound appreciation of the unity of the two testaments."
Benedict is scheduled to meet with Muslim leaders later Saturday at Amman's largest mosque - his second visit to a Muslim place of worship since becoming pope in 2005.
Pope Benedict XVI began his delicate trip to the Middle East on Friday by expressing "deep respect" for Islam and calling for a three-way dialogue of Christians, Muslims and Jews to help peace.
He said that peace efforts were often blocked by partisan interests and that the Church could "help reasonable positions bloom" and that it wanted to engage Jews and Muslims in a dialogue for peace.
"A trilateral dialogue must move forward. It is very important for peace and also to allow each person to live his or her faith well," he said.
The pope arrived in Jordan on Friday, where he began his first Middle East visit as a self-proclaimed pilgrim of peace but could face criticism from Muslims still upset over past comments he made about the Prophet Mohammed.