Al-Aqsa: Israelis storm Jerusalem mosque ahead of tense Yom Kippur holiday
The settlers provocatively toured inside the complex, performing religious rituals and listening to explanations about the temple which some Jews believe used to stand on the site.
The Waqf added that dozens of Israelis blew shofars - musical horns - in between the graves of Muslims in the Bab al-Rahma cemetery near the eastern wall of the mosque.
Local media reported that tight restrictions were applied on Palestinians wishing to enter al-Aqsa, with some having their identification taken away from them and others forcibly ejected from the area.
Ahead of Yom Kippur, which takes place on Tuesday and Wednesday, Israeli authorities raised the state of alert in the occupied West Bank and East Jerusalem.
All major roads were closed in the occupied territories, in addition to the Karam Abu Salem commercial crossing to the besieged Gaza Strip.
The closures are due to be lifted at midnight on Wednesday, before being imposed again on the following Sundays for the Jewish holiday of Sukkot.
Palestinians have become accustomed to increased restrictions on their movement around the time of Jewish holidays.
This year, the closures come amid a heightened campaign of near-daily raids and incursions by Israeli troops in the occupied West Bank.
The army is also preparing to impose a two-day closure on the city of Nablus, blocking all roads leading to it in fear of attacks by armed Palestinian groups.
The northern West Bank city had become the main flashpoint in recent weeks with several settler attacks on Palestinian property reported and a number of shootings at Israeli targets by Palestinian gunmen.
On Tuesday, scores of Israeli settlers gathered on Hawara Street, south of Nablus, performing religious rituals alongside rabbis and the heads of settlement councils.
The Palestinian Red Crescent said that 30 people had been treated late on Monday for breathlessness from tear gas and four for bruising after Israeli army and settler attacks south of Nablus.
Earlier on Monday, two young Palestinians were shot dead and another was wounded after Israeli forces opened fire on a vehicle near Ramallah.
More than 150 Palestinians have been killed by Israeli fire this year, including 49 in the Gaza Strip and at least 100 in the West Bank and East Jerusalem. The death toll in the West Bank is the highest since 2015.