The London based Syrian Observatory for Human Rights has reported that the missile attack was likely carried out by the Israeli military and targeted several government military bases in Al Kiswah situated in the southwest outskirts of the capital.
The Iranian Revolutionary Guard and the Iranian authorities are yet to comment on the reports.
The Syrian state media and Sky News Arabia reported Syria's air-defense system also intercepted two Israeli surface-to-surface missiles.
It is not clear whether the Syrian army or Iranian and Hizballah militias were targeted in the strike.
The incident comes amid escalating tensions between Israel and Syria.
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The source added that an Israeli fighter jet was flying at a low altitude over Lebanon's Baalbek region near Syria's border when the Syrian missiles were launched.
SANA says the missile attack occurred shortly after midnight on Friday and caused material damage. In satellite images published by the BBC, several buildings that appear to be storage facilities - for vehicles or weapons - are seen along a staging ground, with other buildings, one of them appearing to be a headquarters, adjacent.
This follows a row of seemingly random attacks on Syria by the hostile Israeli Defense Forces, which often target positions near the Golan Heights but have since expanded their operating territory to attack more high-value targets.
Previously, Israeli Prime Minister Benjamin Netanyahu has said that it would not allow Iran to establish any military presence in Syria.
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