There was increased police presence in the Old City during the Muslim celebration of Qadr Night, marking the night when the Quran supposedly came down from Heaven.
Police dispersed several dozen rioters on their way out of the al-Aqsa compound, arresting one, with additional arrests expected later in the day.
Worshippers at the scene also attempted to quell the disturbance, preventing rioters from causing further damage before police arrived.
Police released a statement, saying they would, "continue to allow freedom of worship while taking measures against the rioters and lawbreakers harming the multitude of worshippers at the site."