The attack late Wednesday night was near Hader at the frontier of the Israeli-occupied Golan Heights and caused only material damages, Syrian state news agency SANA cited a military source as saying.
Israeli Prime Minister Benjamin Netanyahu told Russian Federation on Wednesday that Israel does not intend to threaten Bashar al-Assad's regime and asked Moscow to work to remove Iranian forces from Syria, an Israeli official said.
The drone shot down by the IDF was an intelligence-gathering aircraft and belonged to the Syrian government and its remains have already been retrieved just south of the Sea of Galilee, nearly ten kilometers (six miles) inside Israel, an army spokesman told reporters.
A Syrian woman holds a baby as she walks into a checking room just after they crossed the armistice line to the Israeli-occupied Golan Heights to get medical treatment in Israel, July 11, 2018. The plateau is not recognised internationally as Israeli territory.
Israel has been on high alert recently as Syrian rebels have advanced on the Golan area.
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The drone "infiltrated the Israeli border from Syria", the Israeli military statement said, without immediately elaborating on whether the shoot-down took place over the Golan.
In the ensuing years, Israel has rarely commented on targeted strikes against Iranian convoys attempting to deliver weapons to Hezbollah in Lebanon or airstrikes against Iranian military bases in Syria.
Spillover fire from Syria's civil war has occasionally landed in the Israeli-controlled Golan Heights.
"We will discuss Syria, we will discuss Iran, we will discuss Israel's security needs", Netanyahu told reporters before departing.
Israeli Prime Minister Benjamin Netanyahu traveled to Moscow Wednesday to communicate Israel's security concerns in Syria and Lebanon to Russian President Vladimir Putin.
Israel seized a large swathe of the Golan Heights from Syria in the 1967 Six-Day War and later annexed it, in a move never recognised by the global community.