The Temple Mount was closed to visitors after Muslim worshippers threw stones and firebombs at police offers guarding the Mughrabi gate near the Western Wall Plaza.
Two Israeli police officers were injured in the Sunday morning riot, which began when the site, which is holy to both Muslims and Jews, was opened to visitors.
Police entered the Al-Aksa Mosque compound and used stun grenades and rubber bullets to break up the rioters, according to reports.
Extra police units were posted on the Temple Mount to prevent further disturbances. Police were set to hold a security assessment later on Sunday to determine if the Temple Mount can be reopened to visitors.
The site is overseen by the Muslim Wakf, the Muslim religious administration charged with managing the Temple Mount site. Jews generally are not permitted by the Wakf to pray or bring any ritual objects to the Temple Mount when they visit.
Temple Mount Closed After Violence Flares