It was the most serious incident to take place on the strategic plateau since the outbreak of the Syrian civil war in 2011.
"A warplane that penetrated Israeli territory was successfully shot down a short while ago by the air defence systems along the Syrian border," a military statement said, without giving further details.
Army radio said it was apparently a MiG-21 fighter jet which was shot down by a surface-to-air Patriot missile, with the wreckage landing on the Syrian-controlled side of the plateau.
The Assad regime has been hitting back with frequent air strikes in a bid to retake control of the plateau. Some have been close to Israeli positions.
Since the uprising erupted more than three years ago, the plateau has been tense, with a growing number of rockets and mortar rounds hitting the Israeli side, most of them stray, prompting occasional retaliatory fire.
But there have been several incidents of intentional fire, one of which killed an Israeli teenager in June.
Some 510 square kilometres of the Golan remain on the Syrian side of the ceasefire line, with UN forces overseeing a buffer zone stretching some 70 km from Lebanon in the north to Jordan in the south.
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