"The IDF (Israeli army) targeted nine Syrian army positions in response to the earlier attack that originated in Syria killing an Israeli teenager and injuring two other Israeli civilians," an army spokesman said.
The targeted sites include Syrian military headquarters and launching positions, and "direct hits were confirmed", the statement added.
"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," the spokesman Peter Lerner concluded.
Israel's defence ministry and the army said the boy, 13, died when a blast hit the car he was travelling in with his father and another contractor, both of whom were wounded.
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The Israeli army called the explosion "an intentional attack" on a civilian vehicle by forces inside Syria, with a senior spokesman telling reporters Israeli tanks had fired at Syrian army posts in response.
It was not clear whether there were any casualties on the Syrian side.
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.