Israel said the targets of the strikes, its largest in Syria since the 1973 war, included weapons storage, logistics sites and intelligence centres used by elite Iranian forces.
The Israeli military on Thursday said it attacked almost all of Iran's military installations in Syria in response to an Iranian rocket barrage on Israeli positions in the occupied Golan Heights, in the most serious confrontation between the bitter enemies to date.
European governments tried for months to persuade Trump to stick with the deal but failed, and now fear it will raise the risk of conflict in the region.
The immediate tensions stem from an Israeli air strike on what they claimed was an Iranian drone facility at the so-called T-4 air base, near Palmyra, on 9 April, which reportedly killed several Iranian military advisers. He asserted that Iran will not be allowed to establish a military presence in Syria. The Israeli security cabinet is satisfied with the massive operation and said Iran got the message.
It blamed Iran's Quds force, adding that Israel's anti-missile system intercepted four, while the rest did not land in its territory.
The strikes were the heaviest carried out by Israel on Syria in decades.
Tension has been building.
The secretary-general of the United Nations, Antonio Gutteres, has called for an immediate halt to "all hostile acts" to avoid "a new conflagration" in the Middle East after Israeli forces bombed Iranian targets inside Syria.
Israeli Prime Minister Benjamin Netanyahu was a sharp critic of the Iran nuclear deal. This phase may not last long and does not mean that the Iranians have any faith in the European Union states keeping the accord alive.
There may not be much Iran can do about President Donald Trump's withdrawal from the nuclear deal, but across the Middle East it has a variety of ways it can hit back at the United States and its regional allies.
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Germany, France and Britain have vowed to keep the 2015 nuclear agreement alive following the USA decision to walk away. Israel's Defense Minister warned: "We always have to be on guard".
Russian Federation - which is alone in having close relations with both Iran and Israel - has sought to position itself as a mediator to prevent further escalation. The revolution's leader, Ayatollah Khomeini, declared Israel an "enemy of Islam" and cut all ties.
"The Israelis want to make this into an Iran-Israel thing, but it isn't".
But unlike Israel and its Arab neighbors, the two countries have never had a direct confrontation.
Mr Netanyahu evidently wanted to reassure Mr Putin that Israel is acting against Iran and is not trying to make a late-in-the-day attempt to change the outcome of the Syrian civil war, which is so far ending with a victory for Russia's ally President Bashar al-Assad.
But if they do escalate, the region could face one of its worst cross-border conflicts in decades, one that could potentially drag in the United States, a major ally of Israel, and Russian Federation, which is Syria's mightiest ally.
With the capture of the three suburbs, the only area outside government control in Damascus is that of the neighborhood of Hajar al-Aswad and the nearby Palestinian refugee camp of Yarmouk that are partially controlled by the Islamic State group. In Lebanon, Hezbollah would stand ready to support its patron Iran.
Iran sponsors a range of Shia militias in Iraq and has deep ties to the country's economy and political system.
In Yemen, the war in its fourth year is seen as a proxy between Saudi Arabia and Iran and can be a place for Tehran to retaliate and increase pressure.
Yemen's Shia rebels, the Houthis, have fired a series of missiles into neighbouring Saudi Arabia during the three-year-old conflict, most recently on Thursday, a day after Trump's announcement.