Police say they entered the site “to prevent riots”. They were reported to have used tear gas and stun grenades, and were attacked with rocks and fireworks.
Similar clashes took place at the end of July.
Al-Aqsa is one of Islam’s holiest sites and is in the Temple Mount/Haram al-Sharif site also revered by Jews.
The holy compound is a source of religious and political tension between Israel and the Palestinians. It is a frequent flashpoint for violence.
Police spokesman Micky Rosenfeld said forces moved into the Al-Aqsa Mosque compound at around 7am yesterday after police received reports that protesters were planning to disrupt visits to the area by Jewish worshippers and tourists.
He said the protesters barricaded themselves inside the mosque and threw rocks and firecrackers at police. He said police did not enter the mosque, but removed barricades around the building. Suspected pipe bombs were found at the entrance to the mosque.
There were no reports of arrests or injuries. The site was closed for three hours during the standoff.
The hilltop compound is revered by Jews as the Temple Mount, site of the two biblical Jewish temples. Muslims call the site the Noble Sanctuary and revere it as the spot where the Prophet Muhammad ascended to heaven.
The spot is a frequent flashpoint of violence. Since Israel captured east Jerusalem from Jordan in 1967, Jewish worshippers have been allowed to visit - but not pray - at the site.
The area is administered by Muslim authorities and is under Jordanian custody. Muslim authorities view the presence of worshippers and police as a provocation and accuse Jewish extremists of plotting to take over the site.
Abdelazem Salhab, an official with the Waqf, the Islamic body that runs the site, accused police of causing “wide damage” inside the mosque. “They crashed many windows and damaged many carpets,” he said.
“Jews have no rights in the mosque and its courtyard,” he said. “The role of Israeli authorities as the occupying power is protecting this site from non-Muslims who plan to take it over.” Police said they did not enter the site, and that any damage was caused by fireworks ignited by Palestinian protesters inside.
Video later released by police showed Ahmed Tibi, an Arab lawmaker in Israel’s parliament, yelling at officers and calling their presence “a provocation.”
Israeli Prime Minister Benjamin Netanyahu said Israel is committed to preserving the status quo, but would not tolerate violence at the holy site.
“It is our duty and our right to act against lawbreakers to enable freedom of worship at this holy site. We will act assertively against those throwing rocks, firebombs, pipe bombs or any other device,” he said.