"We view very harshly the fire opened last night and this morning, from the direction of Syria on an IDF (Israel Defense Forces) force in Israeli territory," Yaalon said. "We will not allow the Syrian army or any other factor to violate Israeli's sovereignty by firing into our territory."
IDF said no casualties or damage had been reported on the Israeli side of the border, but it was continuing to monitor the situation in the border area.
Syria's opposition network, the Local Coordination Committees of Syria, said rebels were clashing with the Syrian army near the Golan Heights border at the time.
Fighting in the area has intensified in recent days as rebels backed by Nusra Front fighters gain territory.
The radical Islamist al-Nusra Front has emerged as one of the most effective groups in the Syrian resistance, drawing on foreign fighters with combat experience in Iraq and elsewhere.
In December, the U.S. State Department moved to blacklist the rebel group as a foreign terror organization linked to al Qaeda in Iraq.
President Shimon Peres said Israel had high hopes when Syrian President Bashar al-Assad, who trained in London to become a doctor, was elected president. Al-Assad seemed to be "a modern young doctor," Peres said..
"It turned out to be a cover," Peres said. "He tried to build a nuclear bomb and he built a chemical arsenal. Fortunately, the nuclear installation is destroyed. Unluckily the chemical arsenal remained."
He added, "What's happening in Syria is a tragedy for Syria."