Moreover, the Syrian army has repeatedly seized huge quantities of Israeli-made weapons and advanced military equipment from the foreign-backed militants inside Syria.
In a rare move, the Israeli military admitted to the bombing raid and said that Syria launched several missiles in retaliation, which triggered rocket sirens in the Jordan Valley.
The incident is the most significant military squabble between the Syria and Israel since the Syrian civil war started in March 2011.
Also on Friday, Israeli Prime Minister Benjamin Netanyahu acknowledged Israeli air strikes in Syria, making a "rare statement on the matter", according to Israeli media.
"All of our aircraft returned to their bases without any threats posed by Syrian air defenses", Israeli army spokesman Avijaa Odraei told Anadolu Agency.
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An Israeli army statement said "several anti-aircraft missiles" were fired following the raid but that none hit their targets.
In response, Syrian forces fired anti-aircraft missiles at the Israeli jets, saying they downed one aircraft and hit another. However, Israel's Arrow defence system is created to intercept long-range ballistic missiles high in the stratosphere, so it remained unclear why the system would have been used in this particular incident. One of the missiles was intercepted by its aerial defense systems, the IDF added. Hezbollah and Israel fought a 34-day war along the Israel-Lebanon border in 2006 and both sides say they are prepared for another.
The skies over Syria are now crowded, with Russian and Syrian aircraft backing the regime's forces and a US-led coalition striking Isis and al-Qaida targets. Last April, Netanyahu confirmed that Israel had struck Syria "dozens of times", breaking with the policy of remaining quiet about involvement in its war-torn northern neighbor.
He warned that "every time we'll identify a smuggling attempt we will act to foil the shipment of tie-breaking weaponry". The Israeli army did not reveal the target of its overnight airstrikes.
Illustrative: Smoke rises following an explosion in Syria's Quneitra province as Syrian rebels clash with Assad regime forces, seen from the Golan Heights in 2014. "None of the aircraft was hit, but one of the missiles was intercepted north of Jerusalem by an Israeli missile defence system".