Residents in Damascus said explosions could be heard near the capital; there were no immediate reports on casualties.
Syrian state TV gave no further details, though said one of the Israeli missiles was shot down near the Damascus suburb of Aqraba.
There was no immediate comment from Israel, who told Fox News they don’t comment on foreign media reports of airstrikes attributed to the Jewish state.
In neighboring 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.
Fox News correspondent Trey Yingst reported Sunday that explosions were also heard in the city of Homs, in western Syria, that is also home of a base that is linked to Iran.
The Britain-based Syrian Observatory for Human Rights, an opposition war monitoring group that has activists around the country, said the missile attack targeted Iranian and Syrian military positions near Damascus.
Israel has repeatedly struck Iran-linked targets in Syria in recent years and has warned against any permanent Iranian presence on the frontier.
Last month, the Israel Defense Forces (IDF) said it carried out “wide-scale strikes” of targets in Syria belonging to Iranian forces and the Syrian regime, in response to four rockets launched into the Israeli-controlled Golan Heights last month. The targets reportedly included missile launchers, warehouses that stored weapons, command centers and bases.
Also 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.
The Israeli airstrike killed Bahu Abu al-Atta and his wife in their home in eastern Gaza, Lt. Col. Jonathan Conricus, an IDF spokesman, said.
Syrian officials said another Israeli airstrike in Damascus targeted another Islamic Jihad commander, Akram al-Ajouri, who was not harmed. Israeli warplanes fired three missiles at al-Ajouri's home, killing his son and granddaughter, according to Syria's state-run news agency.
The attempt was seen as underscoring the risk of escalation at various pressure points across the volatile region.
Iran has forces based in Syria, Israel’s northern neighbor, and supports Hezbollah militants in Lebanon.
The Associated Press contributed to this report.