The airstrike came as violence resumed in the Damascus suburbs after days of calm while the government and opposition delegations attended peace talks in Geneva.
SANA, the state news agency, said the missile attack caused material damage but gave no details. The report also said that Syrian air defenses shot down two of the Israeli missiles.
Israel has carried out a number of airstrikes against suspected arms shipments believed to be bound for Lebanon's Hezbollah militant group, which is fighting alongside Syrian government forces in the civil war.
Israel has also struck several Syrian military facilities since the conflict began, mostly near the Israeli-occupied Golan Heights. In September, Israeli warplanes hit a military position near the Mediterranean coast in western Syria, killing two soldiers and causing material damage.
Rami Abdurrahman who heads the opposition's Britain-based Syrian Observatory for Human Rights said the missile attack targeted an arms depot near Kiswah where the Syrian army's 1st Division is based.
He added that there is Iranian and Hezbollah presence in the area but added that it was not clear if they were targeted.
Also in the suburbs of Damascus, government forces resumed their airstrikes and bombing of rebel-held areas on Saturday, killing and wounding several people, according to the Observatory and a Syrian Civil Defense search-and-rescue group, also known as the White Helmets.
Syrian state TV also said that the rebels shelled several Damascus neighborhoods, wounding at least three people. It said one of the shells exploded near Al-Mariamiyah Cathedral in the central Bab Touma neighborhood.
The government and opposition resumed peace talks in Geneva on Tuesday. The UN-hosted negotiations paused for the weekend but are scheduled to resume on Tuesday.
The Observatory said six people were killed in Saturday's government airstrike on Arbeen while the White Helmets said airstrikes on the suburb of Harasta killed one person and wounded others, including women and children.
Harasta and Arbeen are in the Eastern Ghouta region, one of the hubs in the uprising against President Bashar Assad in 2011. The area, long besieged by government forces, is now facing the highest recorded malnutrition rate in the country since the outbreak of the war more than six years ago, according to a U.N. report released Wednesday.