The streets of east Jerusalem were calm ahead of the prayers at midday, following an Israeli clampdown on the shrine, which is holy for Muslims and Jews alike, AFP reported.
Clashes erupted when Israeli police on Wednesday night shot dead a Palestinian accused of trying to kill a Jewish hardliner.
The closure was the first for decades and prompted a spokesman for Palestinian president Mahmud Abbas to condemn the move as an Israeli "declaration of war".
Police spokeswoman Luba Samri said that because of fears of unrest at the midday prayers, entry for Muslim men would be restricted to those over 50.
Additional police were deployed around the Al-Aqsa compound in the heart of the Old City, with local media reporting the presence of some 3,000 officers, three times more than usual.
The Al-Aqsa mosque compound -- known to Jews as the Temple Mount -- is the third holiest site in Islam and Judaisms holiest.
The clashes subsided late Thursday with a few sporadic confrontations between stone-throwing Palestinians and police firing rubber bullets and tear gas. Three Palestinians were arrested, Samri said.
The funeral of the Palestinian passed off without incident, she added.
Jerusalem has been shaken by months of unrest sparked by the murder of a Palestinian teenager in July in revenge for the killings of three Jewish teenagers in the West Bank.
A 50-day war between Israel and Palestinian militants in Gaza in July and August intensified protests and clashes in the Holy City.
(U.H-RN)
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