Syria's military said it had downed one of the Israeli planes and hit another as they were carrying out the pre-dawn strikes near the famed desert city of Palmyra that it recaptured from jihadists this month.
One missile was intercepted by Israel's Arrow air defence system, Israeli media reported.
While the Syrian Army has achieved major victories against the terrorist groups in the battlefield and has forced the militants to withdraw from many areas, the Israeli aerial operations inside Syria signify the striking similarity between the stances of Tel Aviv and those of terrorist groups and lay bare the "the occupying Israeli regime's illegitimate interests in strengthening Takfiri-Zionist terrorists", he deplored. "Every time we identify a transfer like this, we will work to prevent the transfer of game-changing weapons".
"I can say that the sirens were the result of the incident", an Israel Defense Forces spokesperson told Sputnik, referring to the launch of missiles at Israeli planes that carried out attacks on targets in Syria.
"We shall make great efforts so that this can continue for many more years", he added.
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Israeli Defense Minister Avigdor Liberman has warned Syria that Israel will destroy its air defense system if Syria fires an anti-aircraft missile at Israeli aircraft again.
In a speech on Saturday, Hezbollah chief Hassan Nasrallah accused Israel of intervening in the Syrian civil war on a daily basis, and claimed that Netanyahu "fears the collapse" of the Islamic State group in Syria.
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. Iran claims Hezbollah are fighting Isis, but Israel is concerned that advanced weaponry may be used against it.
In November 2012, Israel fired warning shots toward Syria after a mortar shell hit an Israeli military post, the first time Israel had fired on Syria across the Golan Heights since the 1973 Yom Kippur War.
The Israeli official recognition, which is the first of its kind, also included a statement that the Israeli forces retaliated against a rocket fired from Syria in response to these raids.