The two pilots parachuted to safety before the crash in northern Israel. It is believed to be the first time Israel has lost a jet in the Syrian conflict, BBC reported.
Israel was carrying out strikes after the launch of an Iranian drone into Israel. The drone was intercepted.
It said the drone was identified quickly and was "under surveillance until the interception".
The drone went down on Israeli territory and was "in our possession", Israel Defense Forces (IDF) spokesperson Brig Gen Ronen Manelis said.
The two pilots ejected and were later taken to hospital. Their condition was not immediately known.
Red alert sirens sounded in areas of northern Israel and the Golan Heights due to Syrian anti-aircraft fire.
Residents reported hearing a number of explosions and heavy aerial activity in the area near Israel's borders with Jordan and Syria .
Syrian state media quoted a military source as saying that the country's air defences opened fire in response to an Israeli act of "aggression" against a military base on Saturday, hitting "more than one plane".