Palestinian worshipers in the compound chanted religious slogans at a group of around 30 right-wing Jews who had entered the area via the Moroccan Gate.
Israeli forces raided the compound following the incident and physically assaulted several worshipers, ministry officials said.
The right-wing group was escorted out of the area by Israeli forces without completing their tour.
Earlier, a right-wing Jewish extremist tried to enter the compound by claiming he was a foreign tourist. Israeli police checked the man's documents and prevented him from entering after discovering he was Israeli, ministry officials added.
Al-Aqsa is located in East Jerusalem, a part of the internationally recognized Palestinian territories that have been occupied by the Israeli military since 1967.