Scores of the radicals attended the site – the third holiest in Islam – and worshipped there, according to the Islamic Waqf, the body that administers Al-Aqsa, the official Palestinian news agency Wafa reported.
It comes despite prayer being reserved for Muslims at the compound under the longstanding status-quo agreement. Non-Muslims may however visit the most-sacred Islamic holy place in Palestine.
Israeli extremists routinely storm the site, with many of them wanting to see a Jewish temple built there.
Last month, far-right Israeli National Security Minister Itamar Ben-Gvir stormed the Al-Aqsa compound, with the Palestinian foreign ministry calling his attendance at the site a "serious threat".
Countries including Qatar, Saudi Arabia, Turkey and the UAE also slammed the move.
Palestinians worry about Israeli attempts to split Al-Aqsa in terms of time and space available for use between Jews and Muslims.
Christian and Muslim holy sites in East Jerusalem and Israel often come under attack.
On Thursday, Molotov cocktails were thrown at a mosque in an Israeli city that was built on the land of a former Palestinian village.
The incident happened at the Sayyidna Ali Mosque, located in Herzilya near Tel Aviv, where the village of Al-Haram was once located before its population was displaced during the 1948 Nakba.
The Nakba, Arabic for "catastrophe", saw hundreds of thousands of Palestinians ethnically cleansed from their homes alongside the creation of the Israeli state.
Also on Thursday, a Jewish American tourist allegedly knocked a statue of Jesus over in East Jerusalem's Old City, where Al-Aqsa is also located, according to churchgoers.
"Exodus Chapter 20 says you can't have idols in Jerusalem. This is the holy city," the suspect reportedly said while a guard kept him on the floor.
The suspect was detained by Israeli police after a wooden statue of Jesus was pulled down and damaged in the Church of the Condemnation, where Christians believe Jesus was flogged and sentenced to death.
The police said the arrested man was in his forties and that his mental health was being assessed.
Israel captured East Jerusalem in the 1967 Arab-Israeli War before annexing it in 1980 in a step that has been condemned by the international community.
Palestinians consider the area the capital city of their future independent state.
Agencies contributed to this report.