Israeli warplanes struck nine Syrian army positions on the Golan Heights overnight after a Syrian missile killed a teenager on the Israeli-held side of plateau, the army said early Monday.

It was the second time in three months that Israel had publicly acknowledged striking targets inside Syria, and came just hours after the deadly attack killed a 13-year-old boy.

"The IDF (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.

Sunday's incident, in which a Syrian anti-tank missile struck an Israeli defence ministry car, was the most serious escalation along the ceasefire line since the start of Syria's civil war in 2011, the army said.

The sites targeted in the air strikes included Syrian military headquarters and launching positions, the military said, noting that direct hits were confirmed.

There were no immediate reports of Syrian casualties.

"We hold (President) Bashar al-Assad's regime and the Syrian army responsible for what happens from their territory, and will continue to react forcefully to any provocation", Defence Minister Moshe Yaalon said in a statement.

He said there had been increasing attacks on Israel from Syria, and vowed to extract a "heavy price" from anyone trying to attack Israeli civilians and soldiers -- "whether the Syrian army or terror operatives acting from Syrian territory".

- Car hit by anti-tank missile -

The dead boy killed in Sunday morning's attack was the son of an Israeli defence ministry contractor and was identified as Mohammed Qaraqra, an Arab Israeli from Arabeh village in northern Israel.

The defence ministry said he was killed when a blast hit the car he was in with his father and another contractor, both of whom were wounded.

An army spokeswoman confirmed on Monday that the car had been hit by a Syrian anti-tank missile.

Military sources said it was a defence ministry vehicle used by workers constructing a fence along the ceasefire line.

"Israel's enemies will stop at nothing. They do not shrink from attacking civilians and from killing children," Prime Minister Benjamin Netanyahu said in a telephone conversation with the boy's father.

'They do not distinguish between Jewish and non-Jewish citizens of the State of Israel," he added.

- Deliberate attack -

"Yesterday's attack was an unprovoked act of aggression against Israel, and a direct continuation of recent attacks that occurred in the area," Lieutenant Colonel Peter Lerner, the army's foreign press spokesman, said shortly after the air strikes.

Sunday's attack on the car was "the most substantial incident on the border with Syria since the beginning of the civil war," he had said earlier, noting it was the first time an Israeli had been killed.

Israeli tanks had immediately returned fire at Syrian army posts shortly after the attack, which took place near Tel Khazeka, just south of Quneitra in the centre of the Golan plateau.

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.

Around 510 square kilometres of the plateau remain under Syrian control.

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.

However in March, the army confirmed its warplanes had attacked Syrian army positions just hours after a bomb wounded four Israeli soldiers on the Golan, one severely.