Spokeswoman Luba Samri told AFP the prayers passed off "without incident" a week after Islam's third holiest site saw some 80,000 worshippers throng the compound.
More than 3,000 Israeli police were deployed in the walled Old City, where the compound is located, and elsewhere in occupied east Jerusalem, police said.
Afterwards hundreds of Hamas supporters rallied in support of Egypt's toppled president Mohamed Morsi and against Abdel Fattah al-Sisi, the army chief who ousted him.
The Islamist demonstrators held posters of Morsi, chanting "Morsi is the Egyptian president, Sisi is an American collaborator".
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The Israeli authorities relaxed usual restrictions on entry to Jerusalem by West Bankers for a second week, allowing access to women of all ages and men over 40 years old.
Palestinians from the West Bank and the Gaza Strip are usually barred from Israel and from east Jerusalem, which the Jewish state occupied in the 1967 Six-Day war and then unilaterally annexed.
The Al-Aqsa compound houses both the Dome of the Rock and Al-Aqsa mosque, the third holiest site in Islam after Mecca and Medina in Saudi Arabia.