The military said it had attacked nine targets in response to the killing of a 15-year-old boy in a strike in the occupied Golan Heights on the border between the two countries on Sunday.
Two others, including the boy’s father, an Israeli defence contractor, were injured when a blast hit their vehicle.
Israel called the boy’s death the most substantial incident in the Golan since start of the Syrian conflict in 2011.
It is unclear whether Syrian rebels or government forces were behind the incident.
Israeli military spokesman, Lt Col Peter Lerner, told AP news agency the firing from Syria was “clearly intentional” but it was unclear whether it was the result of mortar fire, a roadside bomb or shelling.
The Golan Heights, a rocky plateau in south-western Syria, was seized by Israel from Syria in the closing stages of the 1967 Middle East War.
The two countries remain technically in a state of war, and UN observers are deployed to monitor a 70km-long (45-mile) demilitarised zone.
Firing linked to the Syrian conflict occasionally reaches the Israeli side of the border fence – some unintentional, some said to be deliberate.
In March, Israel conducted air strikes against several Syrian military targets after a bombing that injured four of its soldiers in the Golan Heights.
Israel had accused the Syrian army of “aiding and abetting” the attack on a patrol near the ceasefire line.
Syria said one of its soldiers was killed in the Israeli military response.
Some of Israeli’s recent air strikes are believed to have prevented the transfer of stockpiles of rockets from the Syrian government to Hezbollah, the Lebanese Shia Islamist movement that supports President Bashar al-Assad.