Another missile reportedly struck Harfa, which is near the border with Israel, and is a Syrian military base.
The Israeli military refused to comment on the raid, but denied a report in Russian media that an Israeli plane had been shot down.
"Our air defense systems repelled an attack by several enemy targets over the Al-Kiswah area in the south of the country and shot them down".
The Israeli army said a missile was sacked at the Golan Heights, but that it remains unclear whether the projectile fell in Israel.
Syrian air defence down several 'enemy targets' in southern Syria – reports
Israeli military forces were deployed to search the area for exploded or fallen ordnance.
"During a Syrian surface-to-air missile launching, one launch was identified towards an open area in the Golan Heights", an Israeli military spokesperson said in a statement.
The latest attack on Al-Kiswah took place in April, when Syrian air defense crews downed 13 missiles.
"Reports of an Israeli aircraft or other Israeli aerial platform being hit are false".
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Israel is widely believed to have been behind a series of airstrikes mainly targeting Iranian and Hezbollah forces in Syria that have joined the country's war fighting alongside the government.
Iran is a key ally of Syria's Bashar Assad and supports a number of militias that have fought alongside the Syrian army and its allies.
Abdel Rahman said Thursday was the first time Syria's air defences had been called into action since the incident on September 17 in which 15 Russians were killed.
Moscow blamed Israel for the incident and supplied Damascus with the advanced S-300 air defense system - something it had previously refrained from doing following requests from Jerusalem.
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Temperatures will range from the 40s north and west to the 50s across southeastern MA, with a gusty southeast wind. Temperatures will quickly fall on Monday and more a more winter-like weather pattern will set up next week.
There was no evidence that the S-300 batteries were used to intercept Thursday night's missiles.
The side behind the attack is not yet clear, but Israel has repeatedly targeted military positions in Syria, including in Kisweh.
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