The Russian made drone was intercepted by a Patriot missile in the demilitarised zone between the Israeli-and Syrian-controlled parts of the Golan, Arab News quoted a military spokeswoman as saying in a statement.
However, the Command of Syria's Allies dismissed such claims, stressing that the drone which the Zionist regime was talking about was operating over the Syrian airspace.
"We can not confirm this report on the drone because Israelis are liars. if Syrians confirm it, Iran will confirm it as well", Brig Gen Hossein Salami said, according to the report.
The Israeli bomber burst into flames and the pilots, who ejected, were injured and evacuated to a hospital. One pilot is in serious condition, while the other one is in stable condition surrounded by his relatives and family members, Israeli media reported.
The Syrian Air Defense forces reportedly employed the Soviet vintage S-200 ( North Atlantic Treaty Organisation reporting name SA-5 Gammon) long range, medium-to-high altitude surface-to-air missile (SAM) system designed in the 1960s to shoot down the F-16I.
The Russian foreign ministry has urged all sides to refrain from escalating the situation.
"Countries and nations have the right to defend their soil, security, and stability in the face of threats", he said.
Israeli strikes in Syria are not unusual, the 's Middle East correspondent Tom Bateman says, but the loss of an Israeli fighter jet marks a serious escalation.
Israeli aircraft then "targeted the Iranian control systems in Syria that sent the UAV into Israeli airspace", according to Mr Conricus.
Israel has largely confined its operations to targeting Hezbollah, the Shia militant group that is a key ally of Iran.
Israel recently has issued several stern warnings about the increased Iranian involvement along its border in Syria and Lebanon.
Iranian and Iran backed Shite forces including the Lebanon's Hezbollah have expressed their support for president Assad in Syria.
A Syrian lawmaker, Feras Shehabi, said the response marked a "major shift in the balance of power in favor of Syria and the axis of resistance". Gen. Ronen Manelis, said in a special statement.
The current violence is the first direct engagement between Iran and Israel, said Sami Nader, head of the Beirut-based Levant Institute for Strategic Affairs. "Iran is dragging the region into an adventure in which it doesn't know how it will end", he claimed in a statement.