Israeli officials argue that Iran's presence in Syria, which is part of an advisory mission requested by the Damascus government, poses a threat to the Tel Aviv regime's security.
"A number of missiles hit arms depots for Hezbollah or Iranian forces", the observatory said.
Russian Federation criticised the airstrike, saying it endangered civilian flights.
The Russian military on Wednesday criticized an alleged Israeli airstrike near the Syrian capital, saying it has endangered civilian flights.
The official spoke on condition of anonymity under standard security protocols.
Israel has previously confirmed carrying out scores of airstrikes in Syria, mostly believed to be aimed at suspected weapons shipments to Hezbollah.
Israel's military spokesman's unit did not confirm the raids, but said in a statement that "an aerial defense system was activated against an anti-aircraft missile launched from Syria".
"We are taking action against it aggressively and powerfully, including in these very days", he said.
The reported attack near Damascus is the first since US President Trump announced last week that the United States will withdraw all of its 2,000 forces in Syria, a move that will leave control of the oil-rich eastern third of Syria up for grabs.
Prime Minister Benjamin Netanyahu attends a graduation ceremony for pilots who completed the Israel Air Force flight course, at the Hatzerim Air Base in the Negev desert, December 26, 2018. It said Syria's air defenses opened fire on "enemy targets", shooting them down.
Konashenkov said the Syrian air defense forces shot down 14 of the 16 precision-guided bombs dropped by the Israeli jets, while the remaining two hit a Syrian military depot 7 kilometres west of Damascus, injuring three Syrian soldiers.
The Israeli army Wednesday evening said they had detonated an "attack tunnel" allegedly dug by Hezbollah into Israel from the southern border-town of Aita Shaab.
The TV, quoting an unnamed military official, identified the warplanes as Israeli.
A screenshot from video on social media purporting to show airstrikes near Damascus on December 25, 2018.
Israel said Tuesday it deployed it's own air defenses against a missile fired from Syria as Damascus attempted to repel the alleged airstrikes.
Turkey said it's working with the United States to coordinate the withdrawal of American forces but remains determined to clear US-allied Kurdish fighters from northeastern Syria.