"At around 11:45 pm (2045 GMT), the Israeli enemy carried out an aerial attack," the ministry said.
It targeted "certain positions in the vicinity of Damascus", but anti-aircraft defences came into action and brought down several missiles, according to the ministry.
An AFP reporter heard explosions in the Syrian capital shortly before midnight local time (2100 GMT).
The strikes were the first on Damascus since late March.
The last Israeli air raids on Syria on May 2 left seven dead.
Since the start of the war in Syria in 2011, Israel has carried out hundreds of air strikes against regime positions as well as Iranian and Lebanese Hezbollah forces, allies of Damascus and arch-foes of Israel.
Israel rarely comments on the strikes on a case-by-case basis, but says it seeks to prevent Iran establishing a foothold on its doorstep.
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