"The aircraft of the Israeli enemy launches a number of missiles at several army positions" in the southwestern province of Quneitra, causing material damage, it said.
Israel shot down a drone that flew in from Syria on Wednesday, the Israeli military said, while Prime Minister Benjamin Netanyahu flew to Moscow to for talks with Damascus's biggest ally about a Syrian advance near the volatile frontier.
The Israeli military said it had hit three targets in retaliation for the incursion of a Syrian drone which it shot down over its air space hours earlier.
"Prime Minister Netanyahu made it clear that Israel will not tolerate a military presence by Iran or its proxies anywhere in Syria and that Syria must strictly abide by the 1974 Separation of Forces Agreement", the Prime Minister's Office said in a statement.
However, the army did not clarify whether the unmanned aerial vehicle was intercepted over the Golan Heights, which Israel occupied during the 1967 war with Syria.
An Israeli military ambulance drives past tanks in the Israeli-controlled Golan Heights, near the border with Syria.
According to Haaretz, the drone was tracked after it went about 6 miles into Israeli territory.
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He says "supplying them on site may face challenges depending on how hard the dives are". We have to wait for the water level to decline.
Since turning the tide of Syria's civil war by intervening militarily in 2015 on Mr Al Assad's behalf, Russian Federation has turned a blind eye to scores of Israeli air strikes against Iranian and Hezbollah deployments or arms transfers, while making clear it wanted Mr Al Assad kept immune.
Israel is particularly anxious about the presence of Damascus ally Iran next door in Syria.
The statement came as the Syrian government retook parts of southern Syria recently, regaining territories lost to rebels during the country's seven-year civil war.
"In recent weeks we are prepared for the possibility of Israeli sovereignty being violated as a result of the fighting in Syria", Israeli Defense Forces spokesperson Ronen Manelis said.
Netanyahu travelled to Moscow on Wednesday for talks with President Vladimir Putin, who in the past has turned a blind eye to Israeli strikes on Iranian and Hezbollah targets in Syria while making clear Russian Federation does not want Assad's rule endangered.
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.