Isreali forces have killed four IS-linked gunmen after they fired at the soldiers in the Golan attack.
The Israeli soldiers were targeted with machinegun fire and mortars and they shot back, before the air force bombed the vehicle carrying the gunmen identified as members of "Shuhada al-Yarmouk, an IS affiliate", said spokesman Lieutenant Colonel Peter Lerner.
The soldiers, from the Golani Brigade, were beyond the fence separating Israeli-occupied Golan from Syria but on Israeli territory, Lerner told AFP, noting none was wounded in the clash.
Since the beginning of the internal Syrian conflict in 2011, stray fire from government and rebel forces has hit Israel, as have attacks by the Lebanese Shiite militant group Hezbollah and its affiliates.
Sunday's clash marked the first time Syria-based jihadists opened fire on Israeli soldiers on territory under Israeli control, according to a retired general, but probably did not mark a change in the strategy of the IS group.
"A direct attack like that on Israeli activities on Israeli side of border -- this is the first time," reserves general Nitzan Nuriel told reporters.
Nuriel said Israel has a policy of preventive action that it uses from time to time in the "grey zone" -- the term he used to describe "pockets between the security fence along the border and the official (demarcation line) between us and our neighbours."
The former director of Israel's Counter Terrorism Bureau said the initiative behind the jihadist attack was "a local decision" and not emanating from a higher echelon, and did not mark a new policy of IS attacks on Israeli forces.
"They know exactly what the Israeli response" would be to attacks, Nuriel said of IS. An Israeli front is "the last thing IS needs at this stage".
Israeli Prime Minister Benjamin Netanyahu praised the soldiers who "successfully repelled an attempted attack on the convergence point of three borders".
"Our forces are prepared on our northern border, and we won't let IS elements or other hostile elements use the cover of the war in Syria to establish themselves next to our borders," he said in remarks relayed by his office.
Israel seized 1,200 square kilometres (460 square miles) of the Golan from Syria in the Six-Day War of 1967 and later annexed it in a move never recognised by the international community.
While avoiding being drawn into the internal Syrian conflict, Israel attacks Syrian military targets when fire, even unintentional, spills over the demarcation line.
The Israeli army holds the Syrian government accountable for any fire from its territory, regardless of the source.