His remarks come after three Jewish minors were ordered to stay away for 15 days by police after they prostrated themselves and recited a biblical prayer during a compound tour.
The Jerusalem Magistrate's Court ruled in favour of the minors on Sunday.
Police argued that the trio had disrupted officers' duties and threatened public order — but Judge Zion Saharai said they had not raised “worry of harm befalling national security, public safety or individual security”, Reuters reported.
Palestinian President Mahmoud Abbas called the ruling “a grave assault against the historic status quo … and a flagrant challenge to international law”.
Under the decades-old “status quo”, Israel allows Jews to visit only if they refrain from religious rites.
Mr Bennett's office said the ruling would be appealed at the higher Jerusalem District Court.
“The magistrate's court decision is focused exclusively on the matter of the conduct of the minors brought before it, and does not include a broader determination regarding the freedom of worship on [Al Aqsa Mosque],” his office said, using the Jewish term for the site Muslims call the Noble Sanctuary.
Jordan, a US-backed Israeli security partner that serves as custodian of Al Aqsa, has also voiced concern about Jewish visits to the compound.
The ruling came a week before nationalist Jews are due to hold an annual flag march through Jerusalem's Old City, marking its capture by Israel in the 1967 Middle East war.
Al Aqsa Mosque compound is a flashpoint of Israeli-Palestinian tension.