The Syrian Observatory for Human Rights said Syrian air defence systems failed to intercept the missiles.
The Britain-based war monitor said an explosion heard at 1 a.m. (2200 GMT Monday) near the airport was caused by missiles fired by Israeli planes from the direction of the Golan Heights.
"It targeted weapons depots and warehouses belonging to non-Syrian militias loyal to the (Syrian) regime," the Observatory said, adding it had no information about casualties or damage.
Iran is a key ally of Syrian President Bashar al-Assad and backs a number of militias, including Lebanon's Hezbollah, fighting in support of Assad.
Asked about the report, an Israeli military spokesman said: "We do not comment on foreign reports."
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