Syrian military air defenses thwarted missiles that Israeli aircraft fired at army positions in Quneitra province in the early hours of Thursday, state media 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.
The military issued a statement warning that it "will not allow any violation of Israeli airspace and will act against any attempt to hurt its civilians".
It was not clear if the unmanned aerial vehicle had strayed across Syria's ceasefire line with Israel unintentionally.
Israel has threatened to open fire at any Syrian government forces that try to deploy in a demilitarised Golan buffer zone set up under a 1974 United Nations -monitored armistice.
Shortly afterward, Netanyahu held a lengthy meeting with Putin in which they established a joint Israeli-Russian team to coordinate military activities and mitigate "misunderstandings". In 1981, the Knesset (the Israeli parliament) adopted the law "On the Golan Heights", which unilaterally proclaimed Israel's sovereignty over this territory.
Israeli Yedioth Aharonoth newspaper reported in April that the Syrian regime had asked Russian Federation to provide it with the S-300 missile defence system, and the Iranians were willing to finance the deal, but, under pressure from the U.S. and Israel, Moscow refused.
In the heaviest Israeli firing since the start of the Syrian War, the UK-based Syrian Observatory for Human Rights, said the strikes killed at least 23 military personnel, including Syrians and non-Syrians.
Israel will not dismiss the possibility of future relations with Syrian President Bashar al-Assad, Defence Minister Avigdor Lieberman said on Tuesday.
"We won't take action against the Assad regime, and you get the Iranians out", Benjamin Netanyahu allegedly told Vladimir Putin during a meeting in Moscow on Wednesday, adding that Israel will continue to protect its border from air and land.
Syria lost control of the Golan Heights to Israel during the Six-Day War of 1967.