Police received intelligence that masked demonstrators were gathering at the mosque. Those inside set up barriers to hinder police from entering then threw rocks and fireworks at them, Israeli police said.
Police quickly removed the barriers and closed up demonstrators inside the mosque.
The clashes occurred ahead of the Jewish New Year, Rosh Hashanah, which begins Sunday evening and goes through Tuesday evening. Al-Aqsa, one of the holiest sites in Islam, is located at the Temple Mount, which is also the holiest site in Judaism.