Palestinian youths are said to have thrown stones at the police, who entered the holy area with full riot gear, which Jews call the Temple Mount, and Muslims al-Haram al-Sharif.
The violence subsided later in the morning, when another group of Palestinians arrived to clean the area ahead of Friday prayers, as thousands of Muslims come to pray in the mosque.
According to the Palestinian Red Crescent, about 30 Palestinians have been injured, 14 of them have been taken to hospital and two are described as seriously injured.
An Israeli policeman was injured when a stone hit her face, according to police.
Similar to last year
Israel has tried to calm the escalating situation by temporarily preventing Jews from praying in the area, which is the third holiest site according to the Muslim faith.
But the Temple Mount is also Judaism's holiest site, and the area is often the subject of conflict.
It is also almost a year since the eleven-day war between Hamas and Israel broke out, with devastating consequences for the Palestinian Gaza Strip in particular.
- Many were worried that it would happen again.
But it does not seem like it this time.
Ramadan is coming to an end, the Jewish Passover is also coming to an end, says Samir Abu Eid in the Morning Studio.
- But a mistake, a small thing, can be the igniting spark that triggers a long and bloody war, he continues.