The Israeli army said Wednesday that it struck near the entrance to the Syrian Ministry of Defence in Damascus.
The strike came as clashes continued in the southern Syrian city of Sweida after a ceasefire between government forces and Druze armed groups collapsed.
Israel has launched a series of airstrikes on convoys of government forces since the clashes erupted, saying that it is acting to protect the Druze.
The Druze religious sect began as a 10th-century offshoot of Ismailism, a branch of Shiite Islam. More than half of the roughly 1 million Druze worldwide live in Syria.
Most of the other Druze live in Lebanon and Israel, including in the Golan Heights, which Israel captured from Syria in the 1967 Mideast War and annexed in 1981.