A similar spillover incident reportedly occurred an hour later, when a second shell hit the same area coming from the Syrian side of the border.
No injuries were reported in the event.
IDF aircraft hit several targets at Syrian army installations in the Golan, destroying buildings and tanks.
"The errant projectile is a result of internal fighting in Syria", the statement read.More news: Ritz-Carlton to Start Luxury Cruise Brand
Two stray mortars from Syria's civil war hit the Israeli-controlled Golan Heights on Saturday night amidst heavy fighting between the Syrian army and rebels near the Syria-Israel border. "Israel holds the Syrian regime responsible for any breach of its borders and will act accordingly".
The Saturday incident is the fifth such incident in the Golan Heights within a week. However, Daniel stressed that when Israel determines that the "spillover fire" was not accidental, the IDF responds in an appropriate manner.
The artillery shells fell at a time when Israeli Prime Minister Benjamin Netanyahu was visiting Katzrin, a town in the Golan Heights about 20 kilometers from where the projectiles landed.
Israel captured the Golan Heights from Syria in the 1967 Six Day War and later extended its sovereignty over the area in 1981 in a move that was never recognized by the global community.