The unmanned aerial vehicle was manufactured in Russian Federation, representative of the Israeli Defense Forces (IDF) Jonathan Conricus told Sputnik.
As per the conditions of the military coordination between Israel and Russia, the IDF apparently contacted Russian headquarters before launching its Patriot defense system.
Israeli Defence Minister Avigdor Lieberman said Israel viewed the incident gravely and would respond to any provocation.
"Moments ago, the IDF used a Patriot Missile to intercept a UAV that attempted to infiltrate Israeli airspace in the Golan Heights", the IDF wrote on Twitter.More news: Real Madrid midfielder Isco: 'Gareth Bale is having a hard time'
The intercepted drone reportedly belonged to the Assad regime and was on an intelligence gathering mission in the Quneitra area of the border.
Israel and Syria are still technically at war after Israel seized around 1,200 kilometers of land in the Golan Heights from Syria during the Six Day War of 1967.
He also called on the Syrian regime to restrain all elements operating from its territory. Syria demands its return.
Last month, Israel struck three Syrian artillery cannons after errant rocket fire landed in the Israeli Golan Heights.