According to the organisation the Israeli strikes targeted different areas in central Syria and near the capital Damascus and its countryside as well as western Swaida and the Daraa-Quneitra-West Damascus countryside triangle.
"Reports about last night's Iranian attacks against Israeli army posts from inside Syria, to which Israel responded by striking against Iranian targets in Syria, are extremely worrying", said a spokeswoman for the bloc's foreign policy chief, Federica Mogherini.
Following the incident, Russia, France, UK, and Germany all called to deescalate the tensions, while the U.S. said Iran was at fault and emphasized Israel's right to "self-defense". Thousands of Iranians took to the streets in cities across the country to protest U.S. President Donald Trump's decision to pull out of the nuclear deal with world powers.
Analysts based in Tehran deny Iran is seeking out direct conflict with Israel.
Then this week, the Iranians fired about 20 rockets at Israeli military positions on the Golan Heights.
Iranian officials have warned they may restart the country's controversial nuclear programme if new USA sanctions are imposed.
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Pointing also to the USA withdrawal from the Paris accord on climate change, Merkel added: "If we always say that, if we don't like things and we can't achieve a new global order, everyone will do what they feel like, that's bad news for the world". Not exactly subtle. But until early Thursday, Iran had never turned its weapons directly on targets inside of Israel.
The Syrian ambassador to China says Damascus will not "hesitate" to avenge Israeli attacks, stressing the nation's right to self-defense against any act of aggression.
Mr Qasemi said the attacks were an attempt by global supporters of rebel groups fighting Syrian President Bashar al-Assad to shore them up after their "many failures" and to try to "tip the scales in their favour". The rockets caused no injuries or damage in Israel.
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.
With the threat posed by the Islamic State increasingly in remission, the danger of the Iranian presence in Syria has moved to the forefront. The IDF blamed the Iranian Revolutionary Guards' Quds Force for the rocket fire.
The re-imposition of sanctions has thrown all that into doubt. Many Iraqis fear escalating tensions between the United States and Iran will destabilise Iraq just as the country is starting to recover.
It feels like a long way from July 2015 when - after more than a decade of painstaking diplomacy - the nuclear deal was finalised by the US, France, Britain, Germany, Russia, China and Iran. European companies, for instance Airbus, are affected too as they buy parts from the US. French Foreign Minister Jean-Yves Le Drian says European companies should not have to pay for the United States decision.