Police were deployed to the compound, known to Jews as the Temple Mount, after clashes a day earlier. Al-Aqsa, the third holiest site in Islam, is also the most sacred place in Judaism. Jews are allowed to visit but not to pray to avoid provoking tensions.
Sunday’s clashes involved Palestinian protesters preparing to defend the mosque during the eight-day Jewish festival of Sukkot, stocking stones inside the shrine and planning to sleep in it.
Young masked Palestinians “threw stones and fireworks at police and border police forces”, who responded with “riot dispersal means”, police said of Sunday’s clashes.
Calm returned to the compound later on Sunday morning and most police were withdrawn, an AFP journalist reported.
Visits by Jews were stopped on Sunday and age restrictions on Muslim men entering the compound lifted for the Muslim holiday of Eid al-Adha, but a ban on under-50s was re-imposed as Sukkot started.
Muslims have been alarmed by an increase in visits by Jews and fear rules governing the compound will be changed.
Recent weeks have seen a series of Jewish holidays during which there has been an uptick in visits by Jews that have sparked repeated clashes. The same situation is feared over Sukkot.
Jews celebrate Sukkot, or the Fest of Tabernacles, to commemorate their journey through the Sinai wilderness to the Holy Land after their Exodus from Egyptian slavery.
According to Biblical tradition, the first and second Jewish temples were located at the site of the Al-Aqsa compound and destroyed by the Babylonians and the Romans.
A hardline Jewish minority has sought to build a third temple.
In past raids, Israeli police have briefly entered the mosque to close the door on stone-throwing rioters inside and restore calm to the compound.
This month over the Jewish New Year holiday, or Rosh Hashanah, police raided the compound to stop what they said were plans by Palestinian youths to disrupt visits to the site.
Clashes occurred over three consecutive days between rioters and police, provoking international calls for calm at the highly sensitive site.
Israel seized Al-Quds, where Al-Aqsa is located, in the Six-Day War of 1967 and later annexed it in a move never recognised by the international community.