The faithful entered the Old City and the mosque compound amidst tighter-than-normal restrictions seeing the prohibition of men under 50 and women under 40, the Palestinian news agency Ma'an reported.
The al-Aqsa mosque compound is the third-holiest site in Islam after Mecca and Medina and is the holiest site in Judaism because it is the location of the Temple Mount, the place where the First and Second Temple are believed by scholars to have stood.
Thousands were turned away performing prayers on the streets, Ma'an reported.
Checkpoints in the West Bank were overwhelmed, with tens of thousands of men and women lining up from the early hours of the morning, awaiting access to Jerusalem.
The compound is inside the Old City in Arab east Jerusalem, which Israel won in the 1967 Six-Day War.