"A terrorist behind the attack in which Rabbi Michael Mark was assassinated on July 1 was killed last night during exchanges of fire with soldiers," the military statement said.
"During the operation to stop Mohamed Fakih, who carried out the attack, he was killed during an exchange of fire with soldiers."
Mark, 48, was killed and three members of his family were injured this month when suspected Palestinian gunmen opened fire on his car, south of Hebron.
The area, where several hundred Jewish settlers live in a tightly guarded enclave in the heart of the city, has been a persistent source of tensions.
Violence in the Palestinian territories and Israel since last October has killed at least 217 Palestinians, 34 Israelis, two Americans, an Eritrean and a Sudanese, according to an AFP count.
Most of the Palestinians killed were carrying out knife, gun or car-ramming attacks, according to Israeli authorities.