The missiles came from the Israeli-occupied Golan Heights and caused some material damage, according to an unnamed military source cited by SANA.
An Iranian military advisor was killed in the attack. Milad Heidari, a member of the Islamic Revolutionary Guard Corps (IRGC) based in Syria, was killed "in a criminal attack by the Zionist regime near Damascus," the IRGC said in a statement carried by Tasnim News.
The IRGC vowed it would retaliate.
The targets of the attack were weapons and ammunition depots belonging to the Syrian military and Iran-affiliated militias southwest of Damascus, reported the UK-based Syrian Observatory for Human Rights (SOHR).
This is the eighth alleged Israeli missile strike on Syria since the start of the year and the sixth in March. At least two Syrian soldiers were wounded in missile strikes early on Thursday.
Syria accuses Israel of carrying out hundreds of airstrikes on regime-controlled areas throughout its 11-year civil war. Primary targets are pro-Iran militias such as Lebanon's Hezbollah, which supports the Syrian army.
Israel rarely comments on airstrikes attributed to it in Syria but has repeatedly warned that it would not tolerate an increase in Iranian presence in the country.
Iran and Israel have been engaged in a long-running shadow war with Israel accused of conducting covert attacks on Iranian military and nuclear facilities, as well as sabotage and cyber-attacks.
Updated at 1:37 pm
