A Border Police officer saw the suspects carrying Molotov cocktails. She ordered them to stop and alerted other officers from the base.
The arrest comes amid rising tensions in Hebron.
On Sunday, an IDF soldier was struck by a Molotov cocktail during clashes between Israeli security forces and Palestinians in Hebron, according to Palestinian reports.
The soldiers responded to the cocktails with fire and hit one of the suspects, identified as Badawi Masalmeh, who later died.
The unidentified attacker reportedly told police that he attacked the synagogue in order to protest Israel.
The border police spokesman said that violent clashes broke out at the camp while they were conducting a security operation there.
Twenty-one fires were set on Thursday in the Gaza vicinity due to burning kites.