Unrest at a highly sensitive Jerusalem holy site led Israeli police to shut off access to it on Tuesday, March 12, after several weeks of tension at the location.
There were no injuries reported from the attack.
The hilltop compound, known as the Temple Mount to Jews and as Haram al-Sharif to Muslims, is central to the Israeli-Palestinian conflict.
Three suspects were arrested and police were seen wrestling a woman to the ground.
The Waqf further claimed Israel had orchestrated the whole incident in a bid to close the holy site, and that it wasn't even clear if a Molotov cocktail had indeed been thrown.
Al-Dibs stressed that large numbers of heavily armed Israeli forces also stormed the Dome of the Rock and repeatedly assaulted Muslim worshipers, both female and male, performing prayers inside, as well as throughout the Al-Aqsa Mosque compound.
Firas Dibs, spokesman for the Waqf, the Jordanian-appointed Islamic body that administers the site, said police had cleared almost all worshippers from the compound.
Several dozen worshippers gathered just outside the compound for impromptu prayers as Israeli police stood watch. It said no soldiers were injured.
Palestinian Authority President Mahmoud Abbas' office condemned "the risky Israeli escalation in the blessed Al-Aqsa Mosque" and urged the global community to intervene after the shutdown.
It is located in east Jerusalem, occupied by Israel in the 1967 Six-Day War and later annexed in a move never recognized by the global community.
Worshippers on the mount have staged protests and clashed with police over the site. "We will continue to act to restore calm on the [Temple Mount]".
The clashes came amid a dispute between Israel and Muslim worshipers over the status of the Bab al-Rahma ("Gate of Mercy") structure within the Al-Aqsa mosque complex, which was closed off by Israel in 2003 over alleged ties between the Islamic society operating there and the Gaza-based terrorist group Hamas.
The Waqf says that because the heritage group is now defunct, the council should regain full access to the building like any other in the holy esplanade.
The Palestinian Authority warned there will be violence if Israel "tampers" with the holy site.
Mustafa Barghouthi, leader of the Palestinian National Initiative movement, also condemned the Israeli attacks on the Palestinian worshippers.