In a statement, the governorate's media office said the occupiers raided the compound's courtyards and performed Talmudic rituals under the protection of Israeli police.
The incident comes a day after Israeli Prime Minister Benjamin Netanyahu, several ministers and thousands of Israeli occupiers entered the Western Wall plaza in East Jerusalem amid tight security.
The incursion also came as the Jewish holiday Yom Kippur begins Sunday evening and continues until Monday evening.
Occupier incursions into Al-Aqsa Mosque have intensified in recent months, particularly during Jewish holidays, amid Palestinian warnings against attempts to impose new realities at the mosque and divide it temporally and spatially.
Israeli far-right police minister Itamar Ben-Gvir visited the flashpoint Al-Aqsa Mosque compound in Jerusalem on Thursday, praising Jewish visitors he said had prayed at the site in breach of arrangements that allow only Muslim prayer there.
His visit drew condemnation from Jordan and Palestinian officials.
The compound in Jerusalem's walled Old City is one of the most sensitive sites in the Middle East. Known to Jews as Temple Mount, it is the most sacred site in Judaism and is Islam's third-holiest site.