Syrian state news agency SANA earlier reported two soldiers had been wounded in the strikes overnight Tuesday-Wednesday. It quoted a military source as saying the bombing targeted "certain positions in the vicinity of Damascus".
The Britain-based Syrian Observatory for Human Rights said the targets included warehouses used by Lebanon's Iran-backed Hezbollah militant group.
The non-government monitoring group, which has a vast network of sources in the war-torn country, said the strikes also targeted positions of the Syrian army's elite Fourth Division near the airport in the town of Dimas.
One Syrian pro-regime fighter and two foreign, Iran-affiliated combatants were killed in the strikes, the Observatory said.
SANA earlier said most of the missiles had been intercepted by Syrian air defence systems, while the Observatory reported the raid had caused fires.
During more than a decade of war in Syria, Israel has launched hundreds of air strikes on its territory, primarily targeting Iran-backed forces and Hezbollah fighters as well as Syrian army positions.
While Israel rarely comments on the strikes it carries out on Syria, it has repeatedly said it will not allow its archfoe Iran to expand its footprint there.
Syria's foreign ministry condemned the attack "in the strongest terms".
In a statement carried by SANA, it called on the United Nations and the Security Council to "take immediate action" to oblige Israel "to desist from these criminal policies".
Tehran says it has sent military "advisers" to support the Syrian army during the war, which has claimed more than 500,000 lives.
Some of those Iranians stationed in Syria have been killed in Israeli strikes.
According to the Observatory, Israel in early July carried out air strikes targeting Hezbollah sites near the government-held city of Homs, killing a member of Iran's Islamic Revolutionary Guard Corps.
The Israeli strikes also targeted a Syrian air defence base in Tartus province, the war monitor said, reporting at least 20 Israeli raids so far this year.
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