The police forces fired rubber-coated bullets and teargas bombs, injuring dozens of Palestinians. At least 12 live-shot injuries were reported.
Ten worshipers were detained during the attack, including a French Muslim woman.
Meanwhile, 428 Jewish settlers were allowed access into al-Aqsa under heavy police protection.
A Jewish settler tried to raise the so-called “israeli flag” in the compound before being arrested by police forces.
The Jewish extremist settler leader Yehuda Glick was among the settler groups.
Jewish visits into the holy site were resumed Thursday after being paused for the last 10 days of the Muslim holy month of Ramadan and the Eid al-Fitr holiday.
Since the early morning hours, zionist police forces were deployed in large numbers in the occupied city of Jerusalem and prevented many worshipers' access into the site to make away for the Jewish settlers.