Israel fired missiles at a military site in the Damascus countryside late on Monday, and Syrian defence systems shot down three of the projectiles, Syrian state news agency SANA said.
Sounds of explosions were heard from the village of Jamraya, west of Damascus, and smoke was seen rising from the area, witnesses told Reuters.
The UK-based war monitor Syrian Observatory for Human Rights said planes bombed a target in Jamraya, where Israel had struck a military research facility back in 2013.
The Israeli military has periodically conducted strikes inside Syria.
On Friday night, an Israeli strike reportedly hit an Iranian military facility south of Damascus. Israel did not claim responsibility for the attack, but SANA said that the Syrian military intercepted Israeli missiles that night.
On Monday, Israeli media outlets published photos captured by an Israeli satellite company showing what was reported to be damage to the base targeted on Friday.
Since the Syrian civil war started in 2011, Israel has also bombed Hezbollah weapon convoys and military officials.
In October, Iran’s military chief General Mohammad Baqeri warned Israel against encroaching on Syrian territories and airspace.
"It's not acceptable for the Zionist regime to violate the land and airspace of Syria anytime it wants," Baqeri said then at a news conference in Damascus.
"We are in Damascus to assert and cooperate to confront our common enemies, the Zionists and terrorists."