The statement said that Syrian air defense shot down a warplane southwest of al-Quneitra, and a drone west of the town of SaaSaa.
But the IDF spokesman`s office called the claims "total lies."
Spokesman Lt. Col. Peter Lerner said that "overnight two surface-to-air missiles were launched from Syria after the mission overnight to target Syrian artillery positions. At no point was the safety of IDF aircraft compromised."
The Israeli mission had been conducted to strike Syrian regime targets after a projectile launched from Syria had struck the Israeli-controlled Golan Heights. No casualties had resulted from the Syrian strike on the Golan Heights, the IDF said.
The Golan has been repeatedly struck with projectiles fired from across the border in southwest Syria, as fighting in the country`s five-year civil war drags on. Last week, three projectiles landed in the Israeli-controlled Golan Heights.
The Israeli strike on Syria came hours after a nationwide ceasefire, brokered by the United States and Russia, came into effect in the war-ravaged country.
In the first 24 hours of the deal, the second concerted attempt this year to halt the grinding civil war, the peace appeared to be holding, although a monitoring group reported a number of violations in and around Aleppo in its early hours.
Israel seized parts of the Golan Heights, a strategic, rocky plateau to its northeast, from Syria in the 1967 Six-Day War.
The international community considers the Golan Heights to be occupied territory and Israeli settlement-building there to be illegal. Syria wants the return of the territory that UN peacekeeping forces have monitored for decades.
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