Israel targeted Syrian military positions early on Thursday after an unmanned drone entered its airspace from the neighboring country the previous day, the military said.
Hours before, Israel said it shot down a Syrian drone that had violated its airspace, underscoring the frontier's volatility.
"The IDF will continue to operate determinedly and decisively against any attempts to hurt Israeli civilians and breaches of Israeli sovereignty".
The anti-aircraft alarm system went off earlier on Wednesday in the Golan Heights, which are controlled by Israel, and in the Jordan River valley.
Israel has been on high alert as Mr Al Assad's forces advanced on rebels in the vicinity of the Golan Heights, much of which Israel captured from Syria in 1967 and annexed in a move not recognised internationally.
Israel is alarmed by Iranian influence in Syria during the seven-year civil war, striking targets it describes as Iranian deployments or convoys of Hezbollah, a Lebanese movement backed by Tehran.
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Israeli Prime Minister Benjamin Netanyahu told Russian Federation on Wednesday that Israel would not seek to topple its ally, Syrian President Bashar Al Assad, but Moscow should encourage Iranian forces to leave Syria, a senior Israeli official said.
The Israeli military said Wednesday that it holds the Syrian regime responsible for what it happens on Syrian territory and warned it against attacking Israeli forces. Damascus also repeatedly denied that the Iranian military has any significant presence in Syria, noting that only the Islamic Republic's military advisers are now present on the ground.
At least some of the missiles were thwarted by Syrian air defences, they said. Israel worries Assad could let his Iranian allies entrench there or that Syrian forces may defy a 1974 Golan demilitarisation.
Israel seized a large swathe of the Golan Heights from Syria in the 1967 Six-Day War and later annexed it, in a move never recognised by the worldwide community.
On Tuesday, Netanyahu met with Russian envoys Alexander Lavrentiev and Deputy Foreign Minister Sergey Vershinin, in Jerusalem, reiterating again Israel's objection to an Iranian presence in Syria. Israel neither confirmed nor denied carrying out that strike.