An Israeli army spokeswoman said the planes early on Wednesday flew over Bashar al-Assad's palace near the city of Latakia, "because the Syrian leadership supports and harbours terrorist leaders, among them Hamas, the kidnappers of the soldier".
Syria said its air defences opened fire on Israeli warplanes that overflew the country, forcing them to flee.
State-run Syrian television said two Israeli planes flew near Syria's Mediterranean coast but did not mention Israel's claim that the planes swooped low over the president's summer residence.
"The overflight by two Israeli planes near the Syrian shores is an aggressive act and a provocation," the television news said, quoting an unindentified information ministry official.
Israeli television reports said the overflights, early on Wednesday morning, created several sonic booms.
The armed wing of Hamas was among the three factions that took part in the cross-border raid from Gaza in which the Israeli soldier was seized on Sunday, but it has not said it is holding him. Israeli leaders have accused Damascus-based Hamas leader Khalid Meshaal of being responsible for the kidnapping.
Israeli television reports said four planes were involved and al-Assad was home at the time.
The flyover was the second time Israel has buzzed al-Assad's summer palace. In August 2003, warplanes reportedly flew so low that windows in the palace shattered.
At the time, Israel said the flyover was aimed at pressuring al-Assad to dismantle Palestinian resistance groups based in his country.
Israeli planes flew over Latakia,
where al-Assad has a residence
In October 2003, an Israeli warplane bombed an Islamic Jihad training base deep in Syria.
It was the first attack on Syrian soil in more than two decades.
The air strike followed a bomb attack by Islamic Jihad that killed 19 Israelis in a restaurant.
Talks with Jordan
Separately, the Syrian leader held talks on Wednesday with Marouf al-Bakhit, the Jordanian prime minister. The talks centred on "new political developments in the region, especially in the Palestinian Territories and Iraq", Syria's official news agency Sana reported.
Al-Bakhit also handed al-Assad a letter from Jordan's King Abdullah II dealing with bilateral relations between the two countries, Sana said.
Al-Bakhit, who arrived in Damascus early Wednesday to co-chair meetings of the Higher Joint Syrian-Jordanian Committee, discussed with al-Assad the committee's role in strengthening bilateral cooperation in all fields, it said.