In a rare confirmation, the Israeli army said in a statement that "a number" of its warplanes had struck positions inside Syrian territory.
The Syrian army high command said the jet was struck by an anti-aircraft missile after it had flown back into Israeli-controlled territory and was one of four planes which "penetrated our air space at 2.40am (12.30 GMT) via Lebanese territory". Syria responded by firing several missiles at the aircraft - one of which was intercepted by Israel's air defense systems.
"This flagrant attack comes to show the Zionist enemy's support to the terrorists gangs of the Islamic State, and a desperate attempt to lift their collapsed morale", the statement contended.
"Overnight IAF (Israeli Air Force) aircraft targeted several targets in Syria". Iran claims Hezbollah are fighting Isis, but Israel is concerned that advanced weaponry may be used against it.
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.
"Several anti-aircraft missiles were launched from Syria following the mission and (army) aerial defence systems intercepted one of the missiles". That could make it harder for Israel to prevent weapons being smuggled from Syria to the militant group Hezbollah in neighboring Lebanon.
The Israeli military, however, later denied the Syrian claims, asserting that all of its fighters had "safely returned to their bases".
The two countries have closely co-ordinated their Syria policies with each other during this period, with Israeli Prime Minister Benjamin Netanyahu and Russian President Vladimir Putin having met five times since the beginning of 2015.
Israel and Syria are still technically at war, though the border had remained largely quiet for decades until 2011 when the Syrian conflict broke out.
A surface-to-air missile (SAM) was intercepted using the Arrow system, created to stop long-range ballistic missiles, reports say.
"Syria made a dramatic shift today as it managed to discover the movements of the Israeli warplanes", Amir said, pointing out that Damascus has broken the equation with the Zionist entity.