"The target was Iranian missiles which were destined for Hezbollah," he told AFP, speaking on condition of anonymity.
The attack targeted a facility just northwest of the Syrian capital, very close to the site of a similar attack late January which was implicitly confirmed by Israel, the source said.
He also confirmed Israel was behind an earlier strike on a target very close to Damascus airport which took place early on Friday, which also struck Iranian arms destined for the Lebanese Shia movement.
"Any time Israel learns about the transfer of weapons from Syria to Lebanon, it will attack," he warned.
According to Syria's official SANA news agency, Sunday morning's attack targeted the Jamraya military research centre near Damascus, in the Eastern Ghouta region.
Following the strike, the Israeli air force went on high alert, although the Jewish state was not anticipating a significant response from Damascus, the source said.
"The air force is now on high alert, the highest in recent years," he said.
Prime Minister Benjamin Netanyahu is due to leave later on Sunday for a five-day visit to China, and the fact that he had not cancelled the trip suggested Israel was not expecting a major response from Syria, he added.
The official Syrian news agency SANA accused Israel of being behind the attack as a show of support for the rebel forces fighting a two-year insurgency against the regime of President Bashar al-Assad.
"This new Israeli aggression is a clear attempt to alleviate the pressure on the armed terrorist groups after our army beat them back in several regions and after the army's victories on the road to recovering security and stability in Syria," said SANA.
The Syrian Observatory for Human Rights watchdog said residents reported seeing aircraft when powerful blasts rocked the area, indicating the strike had caused casualties.
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Atrocities goes towards extremism. Does US not understand
@JohnWV: Dear John, You did not get it altogether right. You should have said the JEWISH STATE OF AMERICA/NATO/AUSTRALIA/CANADA/UN. It is tragic isn't it?
bubba truth allways test like bitter melon.
@JohnWV: Dear John, It is reassuring that you have got it right, and that there are a few intelligent people in the world. Keep up the good work.
where are syrian and iranian tigers now are they sleeping like saddam hussain ??????? or they are just paper tigers .....
@JohnWV. Another off topic anti American rant - yawn.
Israel's Mideast malevolence is a sideshow. It enables the ever increasing Israeli/Jewish control of America's government, finances and military-industrial complex. The Jewish state has occupied not just Palestine, but America too. Our democracy is being methodically destroyed from within and transformed into a world dominating racist ultrapower, the JEWISH STATE OF AMERICA.