Only a warehouse in the Damascus International Airport was damaged, according to the statement.
Syrian state news agency SANA cited a military source saying on Friday that Syrian air defences had shot down Israeli missiles, but a warehouse had been hit.
The Syrian Observatory for Human Rights said "two areas hosting military positions of Iranian forces and the Lebanese Hezbollah movement have been targeted".
"This reflects our consistent policy and the steadfast determination to prevent Iran's military establishment in Syria", Netanyahu said on Twitter on Sunday.
In October, Moscow equipped Damascus with the advanced S-300 surface-to-air missiles, days after Israeli fighter jets attacked Syrian targets using a Russian surveillance plane flying nearby as a shield and hence misleading the Syrian air defenses to shoot it down. The jet crashed in northern Israel and both pilots parachuted out before the impact.
A month-long war in 2006 between Israel and Hezbollah killed more than 1,200 Lebanese, mostly civilians, and more than 160 Israelis, mostly soldiers.
Last September, Israeli Intelligence Minister Israel Katz used a speech to give a rare insight into the country's Syria campaign. While they have at times traded blows within Syria - where Hezbollah has been helping Damascus beat back rebels - the Israel-Lebanon border has mostly been quiet.
The announcement that the operation is ending comes as military chief of staff Gadi Eisenkot steps down at the end of his term. In a New York Times interview published Friday, Eisenkot said that Israel "has struck thousands of targets without claiming responsibility or asking for credit" as part of his showdown with Qassim Suleimani, the commander of Iran's elite Quds Force.
Missile fire is seen from Damascus, Syria on May 10, 2018.