Another four were arrested in skirmishes between Israeli forces and protesters in the surrounding alleys of Jerusalem's Old City. Police fired stun grenades while hitting and kicking demonstrators and journalists as they sought to push back crowds.
Palestinian protesters fear Israel will seek to change rules governing the site, with far-right Jewish groups pushing for more access to the compound and even efforts by fringe organizations to erect a new temple on its grounds.
Israeli Prime Minister Benjamin Netanyahu has said the status quo will be preserved at the sensitive site, but suspicions remain among Palestinians, a sign of the deep mistrust between the two sides.
Non-Muslims are allowed to visit the compound, but Jews must not pray or display national symbols for fear of triggering tensions with Muslim worshipers.
"Some of the young men have been sleeping inside the compound for two or three days to defend it," Umm Mohammed, a 50-year-old among dozens of women protesting outside the gates of the Al-Aqsa compound, told Agence-France Presse.
Non-Muslim visits to the site increase during Jewish holidays, with some 650 visitors on Sunday, according to police. Another 500 visited on Monday during the 7:30 a.m. to 11:00 a.m. visiting hours, police said.
Far-right Israeli Agriculture Minister Uri Ariel was among Jewish activists who visited Sunday, Israeli media reported.
Israeli Defense Minister Moshe Ya’alon last week outlawed two Muslim groups that confront Jewish visitors to the compound, further fueling tensions.
In clashes on Sunday, Muslim witnesses said police entered the mosque and caused damage. Police said only that they closed its doors to lock in rioters throwing stones, fireworks and other objects.
Palestinian president Mahmoud Abbas condemned Sunday's raid, saying sites such as Al-Aqsa constituted a "red line" and adding that "we will not allow attacks against our holy places."
Netanyahu, however, said, "It is our responsibility and our power to act against rioters to allow freedom of worship at this holy place." He said Israel would act "to maintain the status quo and order" at the compound.
Israel seized East Jerusalem, where Al-Aqsa is located, in the Six Day War of 1967 and later annexed it in a move deemed illegal by the international community.
Al Jazeera and Agence-France Presse