The raid followed warnings from Israel that it was ready to act to prevent the revolt against President Bashar al-Assad leading to Syria's chemical weapons and modern rockets reaching either his Hezbollah allies or his Islamist enemies.
A source among Syrian rebels said an air strike around dawn blasted a convoy near the border.
"It attacked trucks carrying sophisticated weapons from the regime to Hezbollah," the source said, adding that it took place inside Syria.
Syrian state television said two people were killed in a dawn raid on the military site at Jamraya, which lies in the 25km strip between Damascus and the Lebanese border.
It described it as a scientific research centre "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 Mr 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 Hezbollah or the Israeli government.
Hezbollah's Al-Manar TV said only that Israeli warplanes had carried out "mock raids" over southern Lebanon last night, close to the Syrian border.
The United States declined all comment. A Lebanese security source said its territory was not hit, though the army also reported a heavy presence of Israeli jets through the night after days of unusually frequent incursions.
Such a strike or strikes would fit Israel's policy of pre-emptive covert and overt action to curb Hezbollah and does not necessarily indicate a major escalation of the war in Syria.
Israeli officials have said they feared Mr Assad may be losing his grip on some chemical weapons, including around Damascus, to rebel groups which are also potentially hostile to Israel.
US and European security sources told Reuters they were confident that chemical weapons were not in the convoy which was bombed.