It is the third instance of cross-border fire from Syria this week.
No soldiers were injured in the incident, which occurred after midnight Monday as soldiers patrolled the border fence near Tel Fares in the central Golan Heights.
The army responded firing a precision Tammuz missile toward the source of fire, Haaretz reported. The missile is able to strike targets up to 15.5 miles away using an electro-optic sensor.
"They fired on our patrol. Whether they knew it was us or not, I don't know, but it's the third time in a row this has happened, at the same place and time. The fire was directed at us," an Israeli defense source told The Jerusalem Post.
In an unrelated incident, Israel's Channel 10 and 2 showed images Monday night of an Israeli army jeep in Syria that the Assad regime claimed is proof that Israel is aiding rebels there.
Israeli military officials noted that the jeep shown in the footage is one that has been out of commission for more than a decade and once belonged to the South Lebanon Army. Israel pulled out of south Lebanon in May 2000.