It was not immediately clear whether Israel held Syrian troops or rebels responsible for what a spokesman for Prime Minister Benjamin Netanyahu said had been a deliberate attack on Israeli patrols in the occupied territory.
Shells have fallen several times inside Israeli-controlled territory during Syria's civil war. Some of the incidents have drawn Israeli return fire.
Syria's southern provinces bordering Jordan and Israel have become an increasingly significant battleground as the capital Damascus - in Syria's south - comes into play and President Bashar al-Assad's forces fight hard to prevent rebel advances.
The Israeli military said one of its vehicles was hit late on Saturday by shooting from across the Israeli-Syrian ceasefire line on the Golan Heights, but no one was hurt.
Israeli military spokesman Lieutenant-Colonel Peter Lerner, said, "Our understanding is that it wasn't stray fire."
After a second incident on Sunday, Israeli soldiers "responded with accurate fire toward the Syrian post from which they were fired on", the military said.
Defence Minister Moshe Yaalon said in a statement that Israel viewed shooting from Syria "with severity" and would not allow "the Syrian army or any other element to violate Israeli sovereignty by firing at our territory".
Israel captured the Golan Heights from Syria in the 1967 Middle East war and annexed the strategic plateau in 1981 in a move that has not won international recognition.
"Any ... fire from the Syrian side will be answered immediately by silencing the sources of fire when we identify them," Yaalon said.
Amos Gilad, a senior Israeli Defence Ministry official, said battles between Syrian government forces and Syrian rebels sometimes take place just a short distance from Israeli lines.
"At times, shells or bullets are fired at Israel. Usually the shooting (from Syria) is not deliberate, but it doesn't matter," he told Army Radio.
"Israel should not be the target of any attack, whether intentional or unintentional - because after all, if you accept something that was unintentional, that could lead to something intentional in the end," Gilad said.
Israel has said for months that it expects Assad's government to fall and has voiced concern that its chemical weapons could fall into the hands of Lebanon's Hezbollah guerrillas and al Qaeda.
Israeli President Shimon Peres has called for Assad to step down.
(Reporting by Dan Williams and Jeffrey Heller Writing by Jeffrey Heller; Editing by Louise Ireland)