The pope angered many in the Muslim world three years ago when he quoted a Medieval text that characterized some of Islam's Prophet Muhammad's teachings as "evil and inhuman," particularly "his command to spread by the sword the faith.
Shortly after giving the speech, Benedict said he regretted the comments offended Muslims.
Ghazi, who is also King Abdullah II's cousin, thanked Benedict for the clarification he issued after the speech that the views did not reflect his own opinion but were instead "simply a citation in an academic lecture."
Benedict told the audience of religious leaders and government officials assembled at the King Hussein mosque Saturday that 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.
The pope said it is often "ideological manipulation of religion sometimes for political ends that is the real catalyst for tension and division and at times even violence in society."
Vatican spokesman Federico Lombardi said the pope did not pray during his visit to the mosque but did stop in a "respectful moment of reflection." He was not asked to take his shoes off when he entered the mosque, which is customary for Muslims, said Lombardi.
Ghazi, who was dressed in a white robe and red and white-checkered headscarf, asked the pope to speak up for Muslim minorities in parts of the Philippines and sub-Saharan Africa who he said were "hard-pressed by Christian minorities."
Benedict expressed "deep respect" for Islam on Friday, when he arrived in Jordan on the first day of his Mideast tour, but his comments in 2006 continue to fuel criticism by some Muslims.
Jordan's hard-line Muslim Brotherhood, the country's largest opposition group, said Friday that they were boycotting the pope's visit because he did not issue a public apology ahead of time as they demanded.
The pope has also had strained ties with Jews that he hopes to improve during his Mideast tour, which will also take him to Israel and the Palestinian territories.
Benedict spoke of an "inseparable bond" between the Catholic Church and the Jewish people Saturday when he visited Mount Nebo, the wind-swept hill overlooking the Jordan valley from where the Bible says Moses saw the Promised Land.
"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 the German-born 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'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.
Despite the disputes, Jewish leaders say Benedict, who served in the Hitler Youth corps as a young man in Germany and then in the army before deserting near the end of the war, has an excellent record in fighting anti-Semitism. He has already visited synagogues in Cologne, Germany, and New York and is expected at Rome's central synagogue later this year.
