It was the second time in 24 hours Israel fired back after stray mortar shells came from Syria, an army statement said.
The mortar shell hit an open area in the central Golan Heights and no one was injured, the army said.
On Sunday, a mortar shell fired from across the Syrian border exploded near an Israeli army post, the army said.
In response, the army said, warning shots and a precision guided missile were fired toward the source of the mortar fire. There were no reports of injuries.
It was the first time Israel retaliated to Syrian fire since a cease-fire agreement was signed between the two countries following the Yom Kippur War in 1973, officials said.
The army said the shelling was reported to the United Nations forces deployed in the region and warned it would respond to any mortar fire or shooting that emanates from Syrian territory.