The police also reportedly detained two guards as they surrounded the compound, entering through the Chain Gate. Scores of worshipers were inside the mosque as it was surrounded, The Russia Today reports.
Dozens of people were removed and assaulted, as reported by the International Middle East Media Center.
Meanwhile, all men below the age of 50 were prevented from entering the mosque grounds, as they headed there for Sunday morning prayers.
Palestinians responded by throwing stones and fireworks and several of the worshippers also barricaded themselves inside the mosque.
The clashes come just hours before the start of the Jewish New Year, Rosh Hashanah, with celebrations to begin at sunset and continue until Tuesday evening.
The Al-Aqsa mosque is considered to be the third holiest place of worship for Muslims. Tensions have been boiling for months at the site in Old Jerusalem, occupied by Israel since 1967.
After the 1967 war when Israel occupied East Jerusalem in violation of international law, Jews were restricted from praying on the Al-Aqsa plaza. Today, the so-called Jewish ultranationalists are pushing Israeli authorities to allow Jewish prayers on the compound outside Al-Aqsa, which stands above the Western Wall, something that irks Jerusalem’s Muslims.
Right-wing Israeli Prime Minister Benjamin Netanyahu is supporting the Jewish ultranationalists.
The Muslim groups say Israelis are trying to change the situation on the ground and give the Jews expanded rights over the holy site.