Syrian state television said two people were killed in a dawn raid on a military site at Jamraya, which lies in the 25-km (15-mile) strip between Damascus and the Lebanese border. It described it as a scientific research centres "aimed at raising the level of resistance and self-defence".
It did not mention specific retaliation but said "these criminal acts" would not weaken Syria's support for Palestinians and other groups engaged in "resistance" to Israel.
Several rebel sources, however, including a commander in the Damascus area, accused the authorities of lying and said the only attacks at Jamraya had been mortar attacks by insurgents.
A regional security source said Israel's target was weaponry given by Assad's military to fellow Iranian ally Hezbollah:
"This episode boils down to a warning by Israel to Syria and Hezbollah not to engage in the transfer of sensitive weapons," the source said. "Assad knows his survival depends on his military capabilities and he would not want those capabilities neutralised by Israel - so the message is this kind of transfer is simply not worth it, neither for him nor Hezbollah."
With official secrecy shrouding the event, few details were corroborated by multiple sources. All those with knowledge of the events - from several countries - spoke anonymously.
There was no comment from the Israeli government nor Hezbollah. Israel's ally the United States declined all comment. A Lebanese security source said its territory was not hit, though the army reported a heavy presence of Israeli jets through the night after days of unusually frequent incursions.