Israeli forces fired tear gas and detained a number of Palestinians on Sunday who were attending prayers after protests erupted in the mosque compound following an announcement that settlers would enter the holy site.
It was the first time in three decades that settlers were allowed into the site during the final days of the fasting month of Ramadan.
Earlier in the morning, Israeli police had deployed hundreds of their forces around the mosque compound and across the city as hundreds of settlers waited at the compound gates to enter.
Reporting from West Jerusalem, Al Jazeera's Harry Fawcett said: "What had been announced was that Jews would not be allowed into the Al-Aqsa Mosque compound because of the sensitivity coming up to the end of Ramadan."
"But what actually took place was that hundreds of what we would expect to be right-wing settler and religious nationalists assembled at the gate demanding entrance.
"Once the police had apparently decided they would be allowed in, protests by Palestinians started and forces moved in to put down the demonstrations. At that point, the Jewish settlers were allowed to come in," said Fawcett.
Video inside the compound showed Palestinians shouting "Allahu Akbar" (God is great), and throwing chairs, and other objects at a doorway before tear gas and stun bombs were thrown at them.