The Jordanian religious authorities who run the compound closed the mosque itself, leaving worshippers to pray in the plaza outside, while Israel limited access to residents of Jerusalem's Old City, an AFP correspondent reported.
The Al-Aqsa mosque is Islam's third holiest site and a national symbol for Palestinians, making it a frequent flashpoint.
The whole of Israeli-annexed east Jerusalem has been cut off from the rest of the occupied West Bank by an indefinite closure aimed at stemming the spread of the virus and movement within it has been restricted.
Authorities around the world have moved to restrict large gatherings, including religious ones.
Synagogues in Israel were allowed to remain open with the chief rabbinate limiting the number of participants in prayers to 10, and many local religious authorities instructing believers to pray at home.
The Israeli health ministry said on Friday it had confirmed 705 cases of coronavirus, while the Palestinian Authority said it had registered 48 cases in the West Bank.
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