The targeted sites include Syrian military headquarters and launching positions, and "direct hits were confirmed", said the statement by Lieutenant Colonel Peter Lerner, the army's foreign press spokesman.
The air raids came after the 13-year-old son of an Israeli defence ministry contractor was killed on the Golan on Sunday.
The Arab Israeli victim was named as Mohammed Qaraqra, from the northern village of Arabeh in the Galilee region, military radio said.
Israel's defence ministry and the army said the boy was killed when a blast hit the car he was travelling in with his father and another contractor, both of whom were wounded.
- 'Unprovoked act of aggression' -
Military sources said the vehicle belonged to the defence ministry and was being used "as part of construction work on the border".
Lerner said the army was "not certain if it was an explosive device, a rocket or a mortar" that hit the car, noting there was a hole in the nearby fence.
"Yesterday's attack was an unprovoked act of aggression against Israel... The IDF will not tolerate any attempt to breach Israel's sovereignty and will act in order to safeguard the civilians of the State of Israel," Lerner stressed.
"This is the most substantial incident on the border with Syria since the beginning of the civil war," he said earlier, confirming it was the first death on the Israeli side.
The army spokesman told reporters that Israeli tanks had fired at Syrian army posts shortly after the attack from Syria.
It was not clear whether there were any casualties on the Syrian side.
Residents in northern Israel heard explosions from the Syrian side of the border, the Israeli news site Ynet reported.
Israel, which is still technically at war with Syria, seized 1,200 square kilometres (460 square miles) of the Golan Heights during the 1967 Six-Day War and later annexed it in a move never recognised by the international community.
Since the Syrian conflict erupted in 2011, the plateau has been tense, with a growing number of projectiles, mostly stray, hitting the Israeli side and prompting occasional armed responses.
Over the past year, Israel has reportedly carried out a series of raids on Syrian and Hezbollah targets, but has not officially acknowledged doing so.
In March, Israeli warplanes attacked Syrian army positions just hours after a bomb wounded four Israeli soldiers on the Golan, one severely.