Two missiles were fired at 06.45 p.m. when government forces were repulsing Al-Qaeda's attacks in the vicinity of the city of Quneitra.
Syria's official news agency SANA said Israel had struck a Syrian army position in the province of Quneitra on the Golan plateau, "causing damage". Israel has not commented on the Sunday report.
The Israeli military said the mortar fire on Friday appeared to be spillover from the raging civil war in Syria.
There have been similar reports of IAF attacks against Syrian targets in recent months, all unconfirmed by Israeli officials.
Israel's army said that two errant mortars hit an open field in the Israeli-held Golan Heights on Friday afternoon, a second such incident over the past hour.
Israel occupied 1,200sq km of the Golan from Syria in the 1967 Middle East war and later annexed it in a move never recognised by the global community.
Forces loyal to Syrian President Bashar al-Assad and Hezbollah have been clashing with rebels not far from the Golan Heights.
The Israeli side is hit sporadically by what are usually deemed to be stray rounds, and Israel has recently taken to opening fire in retaliation.
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