An Israeli spokesman said its aircraft had destroyed 12 military sites, including four allegedly occupied by Iranian forces.
Iran's involvement in Syria in support of Bashar al-Assad in a almost seven-year-old civil war - including the deployment of Iran-backed forces near the Israeli-occupied Golan Heights - has alarmed Israel, which has said it would counter any threat.
An Israeli media report said an Israeli F-16 fighter jet was shot down by Syrian military while targeting what it called Iranian sites responsible for launching a drone into the Israeli side of the Golan Heights.
Israel has looked on with alarm as its arch-enemy Iran has extended its reach in the region during conflicts in Iraq and Syria.
It said its reprisals after the exchange were "large-scale" raids. Many in Israel feared not only that Iran and its allies would entrench themselves near the Israeli border but that Hezbollah had been using the Syrian fighting as a training and that Iran might help the militia upgrade to the use of precision-guided missiles.
Israel has repeatedly warned in recent weeks against the presence of Iranian forces in neighbouring Syria .
According to the Israeli military, the confrontation began with a drone entering its airspace.
"What we're watching is an attempt by the Iranians to shape the situation in Syria as we approach the end of the civil war in a way that serves Iranian interests", said Yossi Kuperwasser, former director general of Israel's Strategic Affairs Ministry and now a senior fellow at the Jerusalem Center for Public Affairs. "Iran only provides military advice to Syria", TV quoted Iran's Foreign Ministry spokesman Bahram Qasemi as saying.
Israel launched air raids in Syria yesterday after one of its fighter jets crashed while under Syrian anti-aircraft fire. Police said the F16 crashed in the Jezreel valley in northern Israel. According to a separate military statement, "multiple anti-aircraft missiles were fired at IAF (Israel air force) aircraft". It later announced that one of the pilots was in serious condition.
Both aircrew managed to eject and landed in Israel.
Eight Israeli aircraft then "targeted the Iranian control systems in Syria that sent the UAV" and confirmed hits, according to Conricus. The Syrian Observatory for Human Rights, a Britain-based monitor of the seven-year civil war, said the Israeli raids had targeted several military bases in the east of the central province of Homs.
It said the bases are used by both Iranian and Russian military personnel deployed in support of the regime. Air raid sirens were triggered in residential areas on Israel's northern border.
Israeli military said it was "monitoring events" and was "fully prepared for further action".
Russia's President Vladimir Putin has urged the Israeli Prime Minister Benjamin Netanyahu to avoid any steps that would lead to a new confrontation in the region, following Israeli airstrikes on Syria.
"This is a serious Iranian attack on Israeli territory".
Last year, Israel pushed back against a partial ceasefire brokered by the United States and Russian Federation, arguing that it allowed Iranian expansion near Israel's borders.
"Security Council members must not stand idly by while Iran is instigating unsafe escalations and violating Security Council resolutions", he said.