Israel says its forces have struck almost all of Iran's infrastructure in Syria, in response to an Iranian rocket attack on the occupied Golan Heights.
The Israeli military said 20 rockets were fired by Iranian Revolutionary Guards at its positions overnight.
It retaliated by targeting what it said were Iranian weapons depots, logistics sites and intelligence centres.
There was no immediate comment from Iran, which has sent troops to Syria to support President Bashar al-Assad.
Syrian state media reported that the army's air defences had repelled an "Israeli aggression" on Syrian territory, shooting down scores of missiles.
But a military source told the official Sana news agency that some missiles had hit a number of air defence battalions, radars and an ammunition depot.
Israel's government has vowed to stop what it considers its arch-enemy's "military entrenchment" in Syria, and it is believed to have carried out several strikes on Iranian facilities since February.
It had been anticipating a retaliatory attack by Iran or its proxies in Syria since seven Revolutionary Guards personnel were killed in a strike on an airbase in April.
What happened in the Golan?
The Israel Defense Forces (IDF) says it has targeted dozens of Iranian facilities with air strikes in retaliation for the attack, which has not been confirmed by Iran.
It said weapons stores, missile launchers and intelligence facilities were all targeted in the wave of strikes overnight.
Syria's state news agency Sana said Israeli missiles had been shot down south of Homs, but reported that a weapons depot and a radar installation had been hit.
Israeli Defence Minister Avigdor Lieberman warned Iran in no uncertain terms on Thursday morning.
"If it rains in Israel, it will pour in Iran," he said.
But Mr Lieberman also added that this was not the beginning of a large confrontation.
"I hope we finished this chapter and everyone got the message," the minister said.
The latest confrontation follows a reported Israeli missile strike on a military outpost south of the Syrian capital of Damascus on Tuesday.
Sana reported that two missiles were shot down in the Kiswah area and that two civilians were killed in an explosion.
But the Syrian Observatory for Human Rights, a UK-based monitoring group, said the missiles hit an Iranian weapons depot, killing 15 pro-government fighters.
Eight members of Iran's powerful Revolutionary Guards force and several other non-Syrian nationals were among those killed, it said.
Israel has occupied most of the Syrian Golan Heights in the 1967 Middle East war and later annexed it in a move not recognised internationally.