Israeli police broke up the early-morning confrontation by using electric batons against the worshipers, the Palestinian news agency WAFA reported.
A worker at the mosque said Moshe Feiglin, who is a member of Israel's ruling Likud party, several rabbis and about 50 other people broke into the mosque to conduct Talmudic rituals in observance of the Sukkot holiday.
The worker said the Jewish group was under police protection.
In a statement issued before the Jewish action, the Al-Aqsa Foundation, a religious endowment and heritage organization, "warned of the consequences," the Ahul Bayt News Agency reported.
The foundation said the mosque belonged to Muslims alone.
Since the beginning of the year, the foundation said the mosque had been entered by 4,700 settlers, nearly 3,250 soldiers and about 220,000 foreign tourists.