"Hezbollah's intelligence headquarters has a branch in Syria, which includes an independent intelligence gathering, coordination, and assessment network," the Israeli military said in a statement, expanding on the Air Force's post on X.
Syria's defence ministry earlier said Israel targeted civilian sites south of the capital and had caused some damage.
Syrian state media SANA said that initial reports indicated the strike had hit the Sayeda Zeinab area.
There were no immediate reports of casualties.
Sayeda Zeinab, a stronghold of the Iran-backed Lebanese armed group Hezbollah and site of a major Shi'ite shrine, has been the target in previous strikes.
Israel has ramped up strikes in Syria since the October 7 attack by militant group Hamas on Israel in 2023 and particularly since the escalation of the Israel-Hezbollah conflict.
It is rare for Israel to comment on the strikes.
Syrian and foreign intelligence sources say Israeli attacks in Syria have killed numerous Hezbollah and pro-Iranian militia fighters based around the eastern outskirts of Damascus and to the south of the city.
The sources say Sayeda Zeinab remains a target due to the presence of high-ranking militia leaders.
Syria's foreign ministry condemned the strike, calling Israeli attacks on civilian areas "criminal" and urging United Nation members to take swift action in "halting Israeli aggression" and holding it accountable.
