The army said Israeli soldiers were targeted Sunday with machinegun fire and mortars and shot back.
"Overnight the (Israeli air force) targeted an abandoned UN building that has been used by the Islamic State as an operations centre along the border in the southern Syrian Golan Heights," an army statement read.
It said the building was the "base for yesterday's attack," which was believed to be the first such direct assault by jihadists on Israeli soldiers in the Golan Heights since Syria's civil war began in 2011.
The army said Israeli soldiers were targeted Sunday with machinegun fire and mortars and shot back. The air force then bombed the vehicle carrying the gunmen, identified as members of the Yarmouk Martyrs' Brigade, a Syrian rebel group that pledged allegiance to IS.
Four of the militants were killed, with no Israeli soldiers injured.
Israeli Prime Minister Benjamin Netanyahu praised the soldiers who "successfully repelled an attempted attack."
"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.
The two countries are still technically at war, though the border had remained largely quiet for decades until 2011.
Since then regular stray missiles have landed in Israeli border areas, but rebel groups and Syrian government forces have largely avoided directly targeting Israeli forces.
Israel attacks Syrian military targets when fire, even unintentional, spills over the demarcation line.