"At around 22:05 pm (1905 GMT), the Israeli enemy carried out an aerial aggression from the occupied Golan Heights, targeting several areas near the capital Damascus," SANA official news agency quoted the statement as saying.
The ministry said "two soldiers were wounded" and Syrian anti-aircraft defences intercepted several Israeli missiles.
An AFP correspondent near Damascus reported hearing bombardments.
A British-based war monitor said Israeli aircraft struck Syrian "regime anti-aircraft defences as well as positions of (Lebanon's Iran-backed) Hezbollah near Sayyida Zeinab" district south of the capital.
Ambulances rushed to the scene after the attacks, added the Observatory, which relies on a network of sources in Syria.
Israel has launched hundreds of air strikes on its northern neighbour since Syria's civil war began in 2011, primarily targeting Iran-backed forces and Lebanese Hezbollah fighters as well as Syrian army positions.
But it has intensified attacks since the war between Israel and Hamas, a Hezbollah ally, began on October 7.
Since then there has been regular cross-border fire between Israel and Hezbollah.
On December 10, two Hezbollah fighters and two Syrian guards working with the group were killed in Israeli strikes in the Sayyida Zeinab district, the Observatory had then reported.
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