Since the start of the war in Syria in 2011, Israel has carried out hundreds of air strikes. AFP
"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 Syrian anti-aircraft defences came into action and brought down several missiles, according to the ministry.
The attack caused only “material damage,” state news agency SANA reported.
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 targeting the international airport in the northern Syrian city of Aleppo. The attack killed one Syrian soldier and put the airport out of commission at the time.
Britain-based opposition war monitor the Syrian Observatory for Human Rights said Israeli said Saturday's attack was the 17th by Israel on Syrian territory since the beginning of the year.
Israel has carried out hundreds of strikes on targets in government-controlled parts of neighboring Syria since the start of the war in Syria in 2011, but rarely acknowledges them.