Israel later implicitly confirms the strike - its first since the start of the Syrian war in 2011.
Smoke rises past a mountain as seen from the Damascus countryside on December 25. "This is a gross violation of the sovereignty of Syria", the Russian ministry of foreign affairs said in a statement. The Syrian regime has branded any rebel groups fighting against its rule as terrorists.
Minister Gebran Bassil also issued instructions to Lebanon's envoy to the United Nations to lodge a complaint against Israel at the Security Council, the statement said.
The Israeli attack was carried out from inside the Lebanese airspace, said the state TV, adding that the air defenses have intercepted a number of missiles, some of which were intercepted while over Lebanon. Israel's air strike was conducted minutes after the leaders boarded a plane bound for Iran.
Syrian media said that most of the incoming missiles were intercepted by its defences, which were filmed firing overnight.
Russian Federation announced it had delivered the S-300 air defence system to Syria in October.
U.S. won't be world's 'policeman,' Trump says during Iraq visit
He is back on Air Force One and will make an another stop, which has not been announced , on his way back to Washington. The trip also comes after Trump announced that he was pulling USA forces out of neighboring Syria.
Several senior Hezbollah officials have been hit by an alleged Israeli airstrike on Syria, Newsweek cited a Department of Defence source as saying on Wednesday.
The strike was also connected with differing reports of the presence of at least one Iranian cargo jet at Damascus Airport.
Three soldiers were also wounded during the attack after explosives hit an arms dump, according to Syrian media.
Israel said it deployed air defenses against a missile fired from Syria as Damascus attempted to repel the alleged airstrikes.
Russia's Defense Ministry has said Israel carried out airstrikes on Syrian targets as two civilian flights were landing in Beirut and Damascus, putting passengers at risk.
Israeli Prime Minister Benjamin Netanyahu has said that Israel would 'continue to act against Iran's attempts to entrench itself militarily in Syria, and to the extent necessary, we will even expand our actions there'.