Syrian air defences opened fire on Sunday night on missiles fired from inside Israel, state media reported.
Syrian state TV gave no further details but residents of Damascus said explosions could be heard near the capital. State TV said one of the Israeli missiles was shot down near the suburb of Aqraba.
An Israeli army spokeswoman said it would not comment on reports in foreign media.
The UK-based Syrian Observatory for Human Rights, an opposition war monitoring group that has activists around the country, said there were three explosions and the attack targeted Iranian and Syrian military positions near Damascus.
There were no immediate reports on casualties.
In neighbouring Lebanon, Israeli warplanes could be heard flying in the country’s airspace at the time of the airstrikes in Syria.
Damascus had said in the past that Israeli warplanes have fired missiles into Syria from Lebanon’s airspace.
Last month, Israel said it struck dozens of Iranian targets in Syria in a “wide-scale” operation in response to rocket fire on the Israeli-controlled Golan Heights the day before.
Israel has repeatedly struck Iran-linked targets in Syria in recent years and has warned against any permanent Iranian presence on the frontier.
Iran has forces based in Syria, Israel’s northern neighbour, and supports Hezbollah in Lebanon.
In November, Israel killed a senior commander of the Palestinian Islamic Jihad, an Iran-backed group in the Gaza Strip, setting off two days of heavy fighting. A separate air raid struck but failed to kill an Islamic Jihad leader in Damascus, underscoring the risk of escalation at various pressure points across the volatile region.