The agency said that "after the aggression," the Israeli military began jamming Syrian military radars.
Israel does not usually comment on reports concerning its strikes in neighboring Syria, though it has recently acknowledged striking Iranian targets there.
Hours after the incident, Prime Minister Benjamin Netanyahu issued a message saying that Israel responds "decisively and forcibly to any attack against us."
"In a systematic and consistent manner we are working to prevent our enemies from establishing attack bases against us nearby," he said during a state memorial ceremony.
Wednesday's incident was the latest in a long string of cross-border incidents along the Israel-Syria frontier. Hours after the reported Israeli strike in Syria, the Israeli military said it observed an unmanned aircraft briefly entering its airspace from neighboring Lebanon.
On June 2, Damascus blamed Israel for attacks on an air force base in southern Syria that killed four soldiers. The Israeli military confirmed it had carried out the strikes on the T4 base in response to rocket attacks into Israeli-held territory.
For years, Israel has remained largely silent about its attacks against Iran and its Shiite proxies operating in neighboring Syria. But in recent months, military and political leaders have become increasingly outspoken about these activities.