He said Muslims and Christians must strive to be seen as faithful worshippers of God "because of the burden of our common history" that has often been marked by misunderstanding.
Iraq Christian minority
Among his audience of religious leaders and government officials was Patriarch Emmanuel III Delly, the head of the Chaldean Church, Iraq's largest Christian denomination, who had travelled to Jordan for the papal visit.
The pope acknowledged his presence and urged the world to make every effort to protect Iraq's Christian minority.
"I urge diplomats and the international community they represent, together with local political and religious leaders, to do everything possible to ensure the ancient Christian community of that noble land its fundamental right to peaceful co-existence with their fellow citizens," he said.
The Islamic Action Front, the kingdom's main opposition party, said before the papal visit to Jordan that Benedict was not welcome unless he apologised for a controversial lecture he gave in 2006.
Benedict had quoted a medieval text that characterised some of the teachings of the Prophet Muhammad as "evil and inhuman".
He did not make an apology during Saturday's speech but Prince Ghazi bin Muhammad, an adviser on religious affairs of King Abdullah, the Jordanian monarch, thanked the pope for the "regret" he had expressed after the lecture in 2006.
The pope said shortly after the lecture that the views did not reflect his own opinion but were instead "simply a citation in an academic lecture".
Earlier on Saturday, the pope visited Mount Nebo, where Biblical tradition says God showed Moses the Promised Land.
Speaking at the slopes of the mountain, the pope called for reconciliation between Christians and Jews.
"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 co-operation," he said.
"The ancient tradition of pilgrimage to the holy places also reminds us of the inseparable bond between the Church and the Jewish people."
During his week-long Middle East visit, Benedict will also travel to Israel and the Palestinian territories.