Zionist forces fired stun grenades, tear gas canisters and rubber-coated steel bullets at Palestinians in the holy site during the clashes.
Zionist media reported that Palestinian youths threw rocks and fireworks at police officers.
Zionist Police had deployed in heavy numbers to secure the visits of Jewish worshipers to the site for the holiday of Sukkot. A group of Israelis also toured the site led by right-wing MK Moshe Feiglin.
Witnesses said Israeli forces raided the site at 6 a.m. following morning prayers.
During the clashes, a fire broke out on carpets near the eastern gate of the compound, Al-Aqsa guards said, as youths and police faced off outside the mosque.
Israeli forces assaulted Aqsa mosque guards during the raids and detained Hajj Nihad Zghayr and an unidentified Palestinian teen.
Palestinian men under 50 and all women were denied access to the holy site for the Jewish holiday, and clashes broke out at the Hatta and Council Gates as Palestinians were turned away from the mosque.
The Al-Aqsa Mosque is sensitive for Palestinians due to its status as the third holiest site in Islam and its location in the heart of the Old City of occupied East Jerusalem.
Israel claims all of Jerusalem as its "eternal, undivided capital," but the international community sees East Jerusalem as Palestinian territory and the capital of a future Palestinian state.