On Monday, Benedict spoke of the "horrific tragedy of the Shoah", the Hebrew term for the Holocaust, disappointing some Jewish religious leaders who said that as a German and Christian, he should have apologised for the second world war genocide.
The pope, born Joseph Ratzinger, was a teenage member of the Hitler Youth, when enrolment was compulsory, and drafted into German forces during the war.
The pope has also disappointed Muslims in the occupied Palestinian territories, with Mohammed Hussein, Jerusalem's grand mufti, calling on the pope to work to end Israeli "aggression" after Benedict became the first pontiff to enter the Dome of the Rock, the third holiest site in Islam.
"We look forward for your holiness's effective role in putting an end to the ongoing aggression against our people, our land, and our holy sites in Jerusalem, Gaza and the West Bank," Hussein said.
Benedict was the first pope to enter the building, which is usually closed to non-Muslims.
Jews consider the plaza on which the gold-domed mosque stands to be their holiest site, the location of the Second Temple destroyed by the Romans in 70 AD.
|Benedict prayed at the Western Wall [AFP]
The visit came a day after a prominent Palestinian sheikh criticised Israel during inter-faith talks with the pope, angering the Vatican.
Sheikh Taiseer al-Tamimi, who heads the Palestinian Authority's Islamic courts, took the microphone after the pope spoke, saying Christians and Muslims must work together against Israel.
"We struggle together and we suffer together from the injustice of the Israeli occupation and its oppressive practices," al-Tamimi said.
Al-Tamimi is known for his scathing attacks on Israel and had not been scheduled to speak.
Federico Lombardi, a Vatican spokesman, criticised the remarks in a statement, calling them "a direct negation of what dialogue should be".
Al Jazeera's Sherine Tadros, reporting on the pilgrimage from east Jerusalem, said: "After Sheikh al-Tamimi made his remarks, most of the room broke out in rapturous applause and that's because Palestinians here share Sheikh al-Tamimi's idea that Israel's occupation really comes to the very heart of what the situation here [occupied East Jerusalem] is all about.
"It affects every facet of the Palestinian life, and there cannot be any talk of unity, inter-faith dialogue or the promotion of peace, without tackling the idea of Israel's 40-year long occupation."
Tadros quoted the Israeli foreign ministry as saying in a statement: "It was regrettable and unacceptable that Sheikh al-Tamimi makes such inflammatory remarks in a meeting that was meant to be about reconciliation."
Israeli papers made similar comments about the incident and praised the pope for walking out after al-Tamimi's comments, reported Tadros.
The pope was in Jerusalem as part of an eight-day tour of the Holy Land - his first since becoming pontiff - that is taking him to sites sacred to Jews, Christians and Muslims in Jordan, Israel and the occupied West Bank.