A senior Israeli source said the aerial assault took out Iranian weapons destined for the Lebanese militant group Hezbollah, which is allied to the Syrian regime.
And a diplomatic source in Beirut told AFP three sites were targeted, including a military facility, a nearby weapons depot and an anti-aircraft unit in Sabura, west of Syria's capital.
The official SANA news agency said Israel had targeted the military research centre at Jamraya in the Eastern Ghouta region, without giving details on casualties or damage.
The Israeli source, who spoke on condition of anonymity, said the target of the attack "was Iranian missiles which were destined for Hezbollah".
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He also confirmed the Jewish state was behind an attack overnight Thursday, which sources told AFP targeted a weapons storage facility at Damascus airport.
This morning, an Israeli army spokeswoman said two batteries of the Iron Dome missile defence system had been moved to the north of the country.
Residents of the upscale Damascus neighbourhood of Dumar, six kilometres away, said the raids caused the ground to shudder and turned the black night sky red.
"It was like an earthquake, the sky was yellow and red," said 72-year-old Najwa.