Only mosque staff and guards were allowed to attend traditional Friday prayers, according to the Waqf, the Islamic body that manages the site. Public gatherings at the compound were banned, although the call to prayer sounded as usual.
The site, known to Muslims as Al-Aqsa and to Jews as the Temple Mount, holds deep religious significance for both faiths.
Nearby, the Western Wall plaza stood empty, with Jewish prayers moved indoors.
Israel remains on high alert after intercepting more than 100 drones reportedly launched from Iran in response.
