Syria’s military said it downed one of the Israeli planes and hit another as they were carrying out the predawn strikes near the desert city of Palmyra, which it recaptured from militants this month.
The Israeli military denied that any planes had been hit.
The Syrian government has made similar claims in the past.
An Israeli army statement said “several anti-aircraft missiles” were fired following the raid but that none hit their targets.
One missile was intercepted by Israel’s Arrow air defense system, Israeli media reported.
It was the most serious incident between the two countries since the Syrian civil war began six years ago.
In April 2016, Netanyahu admitted for the first time that Israel had attacked dozens of convoys transporting weapons in Syria destined for Hezbollah, which fought a 2006 war with Israel and is now battling alongside the Damascus regime.
“Each time we discover arms transfers from Syria to Lebanon we will act to stop them. On this there will be no compromise,” Lieberman said Sunday.
“The Syrians must understand that they are held responsible for these arms transfers to Hezbollah and that if they continue to allow them then we will do what we have to do.”
Lieberman said he did not wish “to interfere in the Syrian civil war or provoke a confrontation with the Russians” but that Israel’s security would remain his top priority.
Russia and Israel’s archfoe Iran has supported Syrian President Bashar Assad’s regime in the war.
Israel opposes Assad, but has sought to avoid being dragged into the conflict.
Israel does not usually confirm or deny individual raids, but it was led to do so this time by the circumstances of the incident, including the firing of the Arrow, Intelligence Minister Yisrael Katz told AFP. He said he believed Assad responded more strongly this time because he feels increasingly confident.
Assad’s position has been strengthened in recent months with his forces reclaiming the whole of Syria’s second city Aleppo, as well as enjoying continuing Russian support.
“He is trying to change the rules. We will not agree to change the rules,” Katz said.
He reiterated what Israel calls its “red lines,” including not allowing advanced weapons to be supplied to Hezbollah and preventing the Golan Heights from being used as a front against it.
Netanyahu has held a series of meetings with Russian President Vladimir Putin in recent months to establish a mechanism to avoid accidental clashes between their forces in Syria.
A “hotline” has been set up between the two countries, but Katz said Russia is not notified in advance of an Israeli strike.
“No one knows before what we are doing,” he said. “We are a sovereign country that acts to protect our security interests.”
He declined to comment in detail on how the “hotline” with Russia worked, but expressed confidence that the two countries could continue to coordinate despite their differing interests.
Israel seized most of the Golan Heights from Syria in the 1967 Six-Day War and occupied it in 1981, in a move never recognized by the international community.
Israel and Syria are still technically at war, though the border had remained largely quiet for decades until 2011 when the Syrian conflict began.
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