Syrian state media said Israeli jets fired on military positions in the southwestern Quneitra province, inflicting material damage.
Russian Federation was already working to distance Iranian forces from areas of Syria near the Israeli-occupied Golan Heights and had proposed that they be kept 80 km (50 miles) away but this fell short of Israel's demand for a full exit, the official said.
The military said it will "continue to operate determinedly and decisively against any attempt to breach Israeli sovereignty and will act against any attempt to hurt its civilians".
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. The Netanyahu government is detemined to keep fighters loyal to Assad and to Iran out of the Syrian Golan border area near Israel.
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The Israeli Defence Force tweeted early on Thursday morning to confirm they had targeted "three military posts" in Syria earlier that evening.
According to Haaretz, the drone was tracked after it went about 6 miles into Israeli territory.
Israel has been on high alert as Assad's forces advance 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.
"The aircraft of the Israeli enemy fired several missiles in the direction of some army positions", Syrian state media cited the military source as saying on Wednesday.
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Israel is particularly anxious about the presence of Damascus ally Iran next door in Syria.
Russian Federation is Assad's big-power backer in the 7-year-old civil war. The 1974 agreement officially ended the 1973 Yom Kippur War between Israel and Syria.
Watched by Israeli soldiers with night-vision equipment, one woman - carrying one child and holding the hand of another - stepped through a gate built into Israel's security fence in the occupied Golan Heights.
Arguing that the Iranian presence in the Arab Republic and its strong foothold on its borders jeopardizes national security, Israel reserved the right to strike Iran-affiliated targets and weapons shipments destined for Hezbollah.
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