Israeli planes were on what the military described as a routine reconnaissance mission over neighbouring Lebanon when an anti-aircraft missile was fired in their direction, a military spokesman said.
The planes returned safely, according to the spokesman, adding it was believed the anti-aircraft battery in Syria was destroyed.
"We hold the Syrian regime responsible for the anti- aircraft fire and any attack originating from Syria," Israeli military spokesman Jonathan Conricus told journalists.
Israel's military said it had no intention to escalate the situation further.
The Lebanese Shiite group is backing Syrian President Bashar al-Assad's regime in the conflict.
Israel and Hezbollah fought a devastating war in 2006.
Today's strike comes with Russian Defence Minister Sergei Shoigu due to visit Israel later in the day. Russia is also backing Assad in the Syrian conflict.
Russia and Israel have established a hotline to avoid accidental clashes in Syria.
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