Syrian state television said on Saturday that the "blatant assault" led to material losses at the site in the countryside near the capital.
An Israeli military spokeswoman declined to comment on reports of the attack.
Earlier in the day, pro-government media outlets had said the air defences were triggered by a missile attack, while people in the capital heard explosions in different areas.
A video was posted on twitter, showing the moment air deference intercepted a missile.
The Syrian Observatory for Human Rights said the missiles, presumably Israeli, struck positions of the Syrian government and its allies southwest of Damascus overnight.
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Syrian state TV reports that the attack caused damage but two missiles were intercepted.
Meanwhile Times of Israel reported the incident quoting Arab media.
Hadashot News reported November 26, that Netanyahu had warned Syrian President Bashar Assad via a third party that Israel would intervene against him in the Syrian civil war if he allowed Iran to establish a military presence in the country.
A report from the BBC in September alleged that Iran had established a military base in Syria, south of the capital; while Iranian forces may not have an overwhelming presence in the country, numerous militias - including Lebanon's Hezbollah - that are aligned with the Syrian regime are bankrolled and armed by the Islamic Republic.
It is not clear whether the Syrian army or Iranian and Hizballah militias were targeted in the strike. According to the reports, Syrian forces fired back at the Israeli forces.