One was located in Damascus's global airport, the other was nearby at the al-Mazzeh airport just outside the capital.
A monitoring group said 11 "fighters" were killed in the air strikes, including seven non-Syrians.
Israel said its aircraft struck dozens of Iranian and Syrian targets in Syria in retaliation for rockets fired at it the day before, which it shot down. "And Immediately our air defense systems thwarted the attack, intercepted the hostile missiles and downed majority before they reached their targets". The Iranian launch followed a rare Israeli daylight air raid near the Damascus International Airport. Damage to the building was deliberately limited and it was not completely destroyed.
SANA says the house was destroyed. "That is what we did tonight towards military targets of the Iranian Quds force and Syrian military targets".
An Israeli official who requested anonymity said a preliminary and yet unconfirmed tally put the number of fatalities at between 10 and 20 military personnel, "about two-thirds of them Iranian and a third (of them) Syrian".
A video purporting to show the aftermath of the attack has emerged on social media.
A general view of the Marjeh Square in Damascus, Syria June 19, 2019.
"During our strike of Iranian & Syrian terror targets, a Syrian air defense missile was sacked despite clear warnings to refrain from such fire".
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Four civilians were wounded, the monitor added.
"Our air defenses were able to intercept the hostile missiles, destroying majority before reaching their targets", said the statement.
Iranian officials have not immediately commented, but Russian Federation called the Israeli strikes a "wrong" move.
He added that Moscow had reached out to its allies regarding the incident, the report said.
"We are preparing for defense and attack, and we will respond to any attempt to retaliate", IDF Spokesperson Hidai Zilberman told reporters on Wednesday. "We will continue operating firmly and for as long as necessary against the Iranian entrenchment in Syria", the IDF said.
Israel has carried out frequent air and missile strikes against targets inside Syria since the country descended into civil war in 2011. "Twenty four hours ago, four rockets were fired at us and downed by the Iron Dome batteries".
The Israeli military would not comment on the explosions in Syria, but Defense Minister Naftali Bennett was convening the top military brass in Tel Aviv to discuss the latest developments.
Israeli Prime Minister Benjamin Netanyahu has issued a series of warnings recently about Iranian aggression throughout the Middle East.