Protected by heavily armed Israeli forces, the storming began at around 7am local time and continued for three hours, as Israelis marked the Jewish holiday of Tisha B'av.
Organised by far-right groups that call for the destruction of Al-Aqsa Mosque, one of the holiest sites in Islam, another round of storming is planned between 1:30pm and 2:30pm.
During the tours in the courtyards of the mosque, settlers performed religious prayers and raised the Israeli flag, in contravention of long-standing agreements on the site.
As part of a decades-old understanding between Jordan – the custodian of Islamic and Christian sites in Jerusalem – and Israel, non-Muslims are not allowed to perform any religious rituals inside the confines of Al-Aqsa Mosque, nor are Israeli symbols allowed to be displayed.
Non-Muslims can visit the mosque under the supervision of the Waqf, a joint Jordanian-Palestinian Islamic trust that manages the affairs of the mosque.
In 2003, the Waqf's management of Al-Aqsa visits was rescinded by Israeli authorities. Since then, Israeli police have allowed settlers and far-right activists to storm the site on a near-daily basis.
Far-right lawmaker Itamar Ben-Gvir led one of the groups that stormed the mosque, in what Palestinians see as a provocation of their feelings and a desecration of the sanctity of the mosque.
Ben-Gvir, who lives in an illegal settlement in the occupied West Bank, is the head of the small Jewish Power party and is associated with the hardline anti-Palestinian Kahanist ideology.
According to local Palestinian media, at least 1,000 Israeli had stormed the site in the morning.
Small groups of Muslim worshippers who were inside the mosque during the raids were assaulted by Israeli forces.
Outside the mosque, located in Jerusalem's ancient Old City, skirmishes occurred between Israeli ultra-nationalists and Palestinian residents.
Some Israeli activists were seen chanting anti-Muslim slogans, such as "Mohammed is Dead," referring to Islam's prophet.
The large Aqsa raids on Sunday were allowed by Israeli authorities despite concerns that they could spark further violence amid the ongoing Israeli military campaign in Gaza.
More than 29 Palestinians, including six children, have been killed in the attacks that began on Friday. At least 253 were wounded, more than half of them women and children, according to the Palestinian health ministry.
On Saturday, several protests were organised by Palestinians to condemn the Israeli aggression in Haifa, Jaffa, Ramallah, Hebron and Jerusalem, among other cities.
A small demonstration at Damascus Gate, an important Palestinian landmark in occupied East Jerusalem, was dispersed by Israeli forces on Saturday evening.
Later in the day, flag-waving Israelis marched throughout the city, reaching Damascus Gate, without any intervention from paramilitary police forces stationed in the area.