The Syrian Observatory for Human Rights said the strike, which hit close to an Iranian cultural centre, had killed 15 people including civilians.
Since the beginning of the war in Syria in 2011, Israel has carried out hundreds of air strikes against its neighbour, primarily targeting positions of the Syrian army, Iranian forces and Lebanon's Hezbollah, allies of the Syrian regime.
Israel's military rarely comments on its strikes against Syria, but regularly asserts that it will not let Iran extend its influence to Israel's borders.
"The strike on Sunday is the deadliest Israeli attack in the Syrian capital," said Rami Abdel Rahman, head of the Britain-based Observatory, which has a wide network of sources inside Syria.
The strike hit in Kafr Sousa, a high-security area of the Syrian capital, which is home to senior security officials, security branches and intelligence headquarters.
"At 00:22 AM (2222 GMT), the Israeli enemy carried out an aerial aggression from the direction of the occupied Golan Heights targeting several areas in Damascus and its vicinity, including residential neighbourhoods," Syria's defence ministry said in a statement.
The strike killed, in a preliminary toll, five people, among them a soldier, and injured 15 civilians, some in critical condition, the ministry added.
Footage posted by state media showed that a 10-storey building was badly damaged during the strike, crushing the structure of its lower floors.
Israel rarely hits residential areas of Damascus.
The attack comes more than a month after Israeli missile strike hit Damascus International Airport, killing four people -- including two soldiers.
The January 2 strike hit "positions for Hezbollah and pro-Iranian groups inside the airport and its surroundings, including a weapons warehouse", the Syrian Observatory for Human Rights said at that time.
At the end of last year, the head of the Israel Defence Forces Operations Directorate, Major General Oded Basiuk, presented the military's "operational outlook" for 2023, saying that the force "will not accept Hezbollah 2.0 in Syria".
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