Israel's military says Iranian forces based in neighbouring Syria fired about 20 projectiles at Israeli positions in the occupied Golan Heights.
It says Israeli defence systems intercepted "some" of the incoming rockets and damage on the Israeli side was minimal. There were no Israeli casualties.
Iran has vowed revenge after blaming Israel for a series of deadly airstrikes on Iranian positions in Syria.
Pro-Syrian government media and activists reported earlier that missiles had been fired toward Israel from southern Syria targeting Israeli positions in the Golan Heights.
Lieutenant-Colonel Jonathan Conricus says Israel views the incident "with severity" and has responded.
Israel has been on heightened alert in recent days, anticipating a possible Iranian retaliation.
Israeli Prime Minister Benjamin Netanyahu has travelled to Moscow where he and Russian President Vladimir Putin will discuss military coordination amid new strikes in Syria blamed on Israel.
His trip came as Syrian state-run media said Israel struck a military outpost near the capital, Damascus, the previous night.
The Britain-based Syrian Observatory for Human Rights said the missiles targeted depots and rocket launchers that likely belonged to Iran's elite Revolutionary Guard in Kisweh, killing nine people.
US President Donald Trump's announcement yesterday that the US would withdraw from the 2015 nuclear deal with Iran has triggered uncertainty and threatened to spark more unrest in the Middle East.
Tensions between Israel and Iran are high over Iran's efforts to expand its military presence in Syria, where the Iranians are a key ally of President Bashar al-Assad.
Repeated airstrikes attributed to Israel have killed Iranian fighters and prompted threats of reprisal from Tehran.