Israel Defence Forces (IDF) said the SA-5 battery, located 50-km east of Syrian capital Damascus, fired a missile at Israeli jets operating over Lebanon this morning.
The fighter jets responded by launching four bombs towards the battery, destroying it, the Israeli army said.
All Israeli aircrafts returned safely to base.
"We're prepared for any possibility," IDF Spokesman Ronen Manelis told reporters.
"This was a Syrian provocation, and we will not allow it. On the other hand, we have no intention of escalating.
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Russia, a close ally of Syria, was updated about the attack in real time, Manelis said.
The incident occurred shortly before an expected visit by Russian Defence Minister Sergey Shoygu to Israel.
Israel believes the reason for the initial Syrian fire at the Israeli planes stemmed from their assumption that they were there to attack, Ha'aretz reported.
The Israeli army spokesperson told reporters that the Israeli planes were on reconnaissance mission in Lebanon, photographing sites for Israel's intelligence.
As per media reports, the Israeli army in September struck a chemical arms plant in Syria. The Syrian army general command confirmed the attack on what it called a "military facility" in which two people were killed and extensive damage was caused but Israel refused to comment on the reports.