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.
Read: Clashes erupt at Al Aqsa mosque compound: Israel police
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Calm returned to the compound later on Sunday morning and most police were withdrawn, an AFP journalist reported.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 reimposed as Sukkot started.
Read: UN Security Council urges calm, restraint at Al Aqsa
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 an been an uptick in visits by Jews that have sparked repeated clashes. The same situation is feared over Sukkot.
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