A government official said on CNN the attack on a military research facility was "an act of war" that the government would not take lightly.
"Syria is a country that does not accept insults and it doesn't accept humiliation," said Omran Zoabi, Syria's information minister. Zoabi added the attack had opened "a wide door for all possible options."
Israel did not confirm it was behind the predawn attack, which shook buildings in Damascus and lit up the sky over nearby Mount Qasioun, which The New York Times said was a strategic stronghold for government forces defending the city.
It marked the second apparent Israeli strike on Syria in three days. Both apparently targeted missiles allegedly bound for Hezbollah forces.
Prime Minister Binyamin Netanyahu did not mention the apparent air attack at his Sunday Cabinet meeting before flying off to China. The military, however, deployed two Iron Dome missile-defense batteries to northern Israel, The Times said.
The Syrian government quickly blamed Israel, and military analysts agreed Syrian rebels did not have the type of firepower required for such an attack.
Israeli Radio said among the eight sites destroyed by the blasts were stockpiles of Iranian made surface-to-surface Fatah 110S missiles, which were suspected of being earmarked for Hezbollah in Lebanon.
The Israelis also denied Syrian claims that an Israeli war plane had been shot down.