It has carried out hundreds of air strikes there against what it says are Iranian military targets and advanced arms deliveries to Lebanon's Hezbollah.
According to Al Hadath TV channel, the Israeli jets attacked Iranian military warehouses near the city airport, used by the Shiite militias Hezbollah fighting on the side of the government army.
Air defense systems "prevented Israeli air strikes from achieving their objectives in the south" of Syria, the report said without giving further details.
Usually silent about its attacks on Iranian targets near its frontier, Israel has lifted the veil this month, a sign of confidence in a campaign waged amid occasional tensions with Syria's big-power backer Russian Federation.
An Israeli military spokesperson told the AFP news agency that the rocket was intercepted by its Iron Dome defence system over the northern Golan Heights, Syrian territory that Israel has occupied since 1967. However, those attacks typically take place under the cover of darkness.
An explosion rocked the southern edge of Syria's capital Damascus on Sunday morning, Syrian state media has reported.
Syrian state media broadcast footage of what it said were the air defenses firing, with bright lights seen shooting across the night sky.
Satellite images revealed by the Intelli Times security blog showed a Boeing 747 Iranian cargo plane unloading equipment at the largest Syrian airport just hours before the attack, and returning to Iran via Iraqi airspace.
"This policy does not change when I'm in Israel, and it does not change when I am in Chad", he added.
Tel Aviv has a bellicose relationship with Damascus' Lebanese ally Hezbollah and Iran, and repeatedly strikes targets in the conflict-torn country.