Syrian Observatory for Human Rights says three non-Syrians were also killed in the Israeli attack.
An Israeli attack killed three Syrian soldiers and injured seven others near Damascus, the Syrian defence ministry has said.
“The Israeli enemy carried out an air strike … from the direction of the occupied Syrian Golan … The aggression killed three soldiers and wounded seven others,” the ministry said in a statement on Friday.
The ministry also said that Syrian air defence forces had intercepted missiles that were launched from the Israeli-occupied Golan Heights, to the west of Damascus.
The Israeli military said it does not comment on foreign reports.
The Syrian Observatory for Human Rights war monitor said that an additional three foreign nationals had been killed, bringing the total number of dead to six and that 10 people were wounded in total.
The monitor, which relies on a wide network of sources inside Syria, said that the raids hit an air force intelligence facility, a high-ranking officer’s office, and a car near the Mezzeh military airport.
The missiles also destroyed an “Iranian weapons depot” in the area of Sayyida Zeinab, the monitor said.
The Syrian government last reported an Israeli attack on July 2, which it said was launched on an area south of the Mediterranean city of Tartus and injured two civilians.
Israel has carried out hundreds of air raids against its neighbour since war broke out in Syria in 2011, on government troops as well as allied Iran-backed forces and fighters from Lebanon’s Shia group Hezbollah.
While Israel rarely comments on individual raids, it has acknowledged carrying out hundreds of them.
The Israeli military says the attacks are necessary to prevent its arch foe Iran from gaining a foothold on its doorstep.
Last month Israeli raids on Damascus International Airport rendered its runways unusable for weeks.
Besides the extensive damage caused to civilian and military runways, the monitor said the attacks had hit nearby warehouses used as weapons depots by Iran and Hezbollah.
Iran said two officers from its Revolutionary Guards were killed in an Israeli air raid in March, prompting Tehran to pledge revenge.
The war in Syria has killed nearly half a million people and forced around half of the country’s pre-war population from their homes.