The facility in Kissweh “presumably” belongs to Hizballah and Iran, said Rami Abdel Rahman, director of the Britain-based Syrian Observatory for Human Rights.
Despite reports of explosions in the area and state TV broadcasting images of fires in the suburb, Syrian state media agency SANA said the army intercepted two missiles.
TV Sanaa quoted a medical source saying that two civilians had died on a highway linking Damascus with the southern city of Deraa as a result of an explosion linked to “the Israeli aggression”, without providing details.
This is not the first time that the area in the southwest of Damascus has been targeted. In December, Israel reportedly bombed military positions in Kissweh, including a weapons depot.
The Tuesday night strikes came hours after US President Donald Trump announced his decision to withdraw from the 2015 Iran nuclear deal, a move praised by Israeli Prime Minister Binyamin Netanyahu.
Netanyahu had been one of the leading critics of the nuclear accord.
His statement came as the Israeli-occupied section of the Golan Heights was placed on high alert due to “irregular activity by Iranian forces” across the demarcation line in Syria.
In recent years, particularly since 2017, Israel has carried out numerous strikes in Syria against the regime of President Bashar al-Assad and his ally, the Lebanese Hizballah.
Israeli missiles left up to 14 fighters dead, including seven Iranians, in Homs last month, two days after the Syrian regime carried out an alleged chemical attack in Douma.
The air base was also targeted by Israel in February.
On April 29, at least 26 mostly Iranian fighters were killed by missiles fired on regime military positions, according to the Observatory.
The strikes, “probably Israeli”, targeted a military airport in Aleppo in the country’s north and Brigade 47 in Hama, where Iranian forces are stationed, the Observatory said.
Occasional clashes have erupted between Israel and the Syrian regime and its Hizballah ally in the Golan Heights, occupied by Israel since 1967.
Israel is concerned that Iran and Hizballah are embedding forces along its border.
In an interview late last month, Israeli Defence Minister Avigdor Lieberman vowed to strike at any attempt by Iran to establish a “military foothold” in Syria.
Iran’s president Hassan Rouhani has previously said the US would regret withdrawing from the accord. He called Trump’s position “illegal” and “psychological war”.