Police say they went into the compound to disperse some 20 masked protesters throwing stones at foreign tourists.
The Islamic body which oversees administration of the area disputes the police account of events.
This is the latest in a series of clashes amid high tensions over religious sites in the past week.
The Jerusalem compound also contains the Western Wall, a sacred site for Jews.
Clashes broke out in the West Bank town of Hebron on Friday over Israel's decision to list two disputed shrines as heritage sites.
Contested site
A Palestinian official said a group of youths had spent the night in the al-Aqsa mosque to prevent what they believed to be Jewish extremists from praying at the sensitive site.
Palestinians and Israelis were injured and several Palestinians were arrested in the brief confrontation on Sunday, police say.
An Israeli police spokesman said calm had been restored to the compound and visits resumed.
The spokesman, Micky Rosenfeld, said Muslim men under the age of 50 had been barred from the site, while older men, women of all ages and children had been permitted to enter.
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