A Syrian Foreign Ministry statement rejected "all forms of foreign intervention" in Syria's internal affairs, without mentioning Israel, and declared Syria's commitment to protecting all Syrian groups "including the noble Druze sect".
It marks the first time Israel had announced a military strike in support of Syrian Druze since Bashar al-Assad was toppled, reflecting its deep mistrust of the Sunni Islamists who replaced him and posing a further challenge to interim President Ahmed al-Sharaa's efforts to establish control over the fractured country.
A Syrian Interior Ministry source told Reuters Israeli drone strikes targeted government security forces, killing one of their members, in the mainly Druze town of Sahnaya on Damascus' outskirts.
The Druze adhere to a faith that is an offshoot of Islam and has followers in Syria, Lebanon and Israel.
In a statement, Israeli Prime Minister Benjamin Netanyahu and Defence Minister Israel Katz said the Israeli military had carried out "a warning operation and struck an extremist group" as it prepared to continue an attack on Druze in Sahnaya.
"At the same time, a message was passed on to the Syrian regime - Israel expects it to act in order to prevent harm to the Druze," they said.
Since Assad was ousted in December, Israel has seized ground in the southwest, vowed to protect the Druze, lobbied the United States to keep the neighbouring state weak and has blown up much of the Syrian army's heavy weapons in the days after he was toppled.
Sharaa, who was an al-Qaeda commander before renouncing ties to the group in 2016, has repeatedly vowed to govern Syria in an inclusive way.
But incidents of sectarian violence, including the killing of hundreds of Alawites in March, have hardened fears among minority groups about the now dominant Islamists.
The sectarian violence began on Tuesday with clashes between Druze and Sunni gunmen in the predominantly Druze area of Jaramana.
It was ignited by a voice recording cursing the Prophet Mohammad and which the Sunni militants suspected was made by a Druze.
More than a dozen people were reported killed on Tuesday, before the violence spread to Sahnaya on Wednesday.
In a statement on state news agency SANA, the director of security for the Damascus countryside said a ceasefire was reached in Jaramana but outlaws had escalated attacks in the Sahnaya area on Wednesday, killing 16 members of the security forces.
Security sources said hundreds of Interior Ministry security forces deployed in and around Sahnaya following an agreement with Druze elders.
Residents said the situation had largely calmed after intense fighting, with only sporadic gunfire heard.
The Interior Ministry has said it is investigating the origin of the audio recording.
Grand Mufti Sheikh Osama al-Rifai, appointed Syria's top Muslim cleric in March, said in a recorded statement that the spilling of any Syrian blood was forbidden.
Geir Pedersen, United Nations special envoy to Syria, is "deeply concerned" by violence in the country, especially in suburbs of the capital Damascus and in Homs, the UN said.
He called for immediate measures to ensure the protection of civilians, and prevent incitement of communal tensions.
The new Islamist-led leadership in Damascus has called for all arms to fall under their authority but Druze fighters have resisted, saying authorities in Damascus have failed to guarantee their protection from hostile militants.
The Israeli government reiterated its pledge to defend Syrian Druze in March after the attacks on Alawites - bloodshed that was sparked by deadly attacks on government security forces and blamed by the Islamist authorities on Assad loyalists.
Israel has a small Druze community and there are also 24,000 Druze living in the Israeli-occupied Golan Heights, which Israel captured from Syria in the 1967 Six-Day war.
Israel annexed the territory in 1981, a move that has not been recognised by most countries or the UN.
The spiritual leader of Druze in Israel, Sheikh Muwafaq Tarif, said he was "closely monitoring" developments in Syria and had discussed them with Israel's defence minister.
Israel also said three Syrian Druze citizens had been relocated from Syria to receive medical treatment in Israel.
