Israeli fighter jets struck near the presidential palace in Damascus, the Syrian capital, early Friday, in what Israel’s prime minister and defense minister said was a message to the Syrian government after a wave of sectarian violence.

In recent days, more than 100 people have died in clashes between Syrian pro-government forces and militants from the country’s Druse minority. The Druse practice a secretive religion with its roots in Islam, and those living in Syria have close ties to the Druse community in Israel.

Friday’s strike is the second time since the violence erupted this week that Israel has intervened militarily.

“This is a clear message to the Syrian regime,” Prime Minister Benjamin Netanyahu and Defense Minister Israel Katz said in a joint statement about the strike. “We will not allow a movement of forces from south of Damascus and any danger to the Druse community.”

In a separate statement, the Israeli military said its warplanes had “attacked the area near the palace of Ahmed Hussein al-Shara in Damascus,” referring to Syria’s president. Mr. al-Shara, a former Al Qaeda affiliate whose rebel coalition toppled President Bashar al-Assad in December, now presents himself as a statesman, but Israeli leaders have expressed wariness.

The strike drew no immediate comment from Syria’s government. Images on social media showed plumes of smoke rising in the night sky in Damascus after Israel’s action. It was not clear what had been hit or how much damage had been done.

By Thursday night, Syrian government representatives had struck accords with Druse leaders in a bid to calm the violence, and leaders in the Druse-controlled Sweida region, previously reluctant to unite with government forces, had expressed openness to doing so.

Israel has offered to protect the Druse in Syria if they come under attack amid the tumultuous transition of power in the country, and it has tried to cultivate relations with Syrian Druse communities. Many Syrian Druse have rejected what they consider potentially destructive foreign meddling.

The Druse community in Israel, however, is pressing for Israel to intervene. Friday’s strike in Damascus came after Druse protesters in Israel blocked highways on Thursday amid mounting demands from members of the community there, some of whom serve in the military, that Israel act forcefully in Syria.

On Thursday, the Israeli military said in a statement that two injured Syrian Druse citizens had been evacuated to receive medical treatment in Israel. Israeli troops had earlier in the week evacuated several other Syrian Druse hurt in the violence.

The Israeli military also said Thursday that its forces were deployed in the southern Syrian region and “prepared to prevent hostile forces from entering the region and Druse villages.”

Mr. Katz, Israel’s defense minister, said on Thursday that Israel would “respond with great severity” if attacks on the Druse did not stop, saying the Syrian leadership bore responsibility for preventing them. “We are committed to defending the Druse,” he added.

On Wednesday, Israel launched airstrikes on Syria and threatened to strike government forces there if clashes persisted between pro-government fighters and Druse militia members. The Israeli military said its aircraft had struck a group of “operatives” whom Israel accused of having “attacked Druse civilians” in the spreading violence around the outskirts of Damascus.

The most recent outbreak of sectarian unrest in Syria began on Tuesday after an audio clip circulated on social media purporting to be of a Druse cleric insulting the Prophet Muhammad. The cleric denied the accusation, and Syria’s Interior Ministry said he was not involved.

Nevertheless, armed Sunni Muslim extremist groups began attacking areas with large Druse populations, including the town of Jaramana near Damascus. Druse militias responded in force, and the government sent security personnel to quell the unrest.

On Wednesday, the clashes spread to another town on the southern outskirts of Damascus, and into Sweida, with fighting continuing until Thursday morning.

Five prominent Druse leaders released a statement Thursday night saying that Interior Ministry personnel and judicial police “drawn from the people” of Sweida “must be activated,” indicating a willingness to join forces with the government.

They also said government forces were being deployed to secure the road from Sweida to the capital. The government also agreed to send reinforcements to protect Jaramana, Druse leaders there said.

The U.S. State Department on Thursday called on Syria’s government to stop the sectarian violence and hold the perpetrators accountable. “The recent violence and inflammatory rhetoric targeting members of the Druse community in Syria is reprehensible and unacceptable,” said a spokeswoman, Tammy Bruce. “Sectarianism will only sink Syria and the region into chaos and more violence.”

There are more than one million Druse across the Middle East, mostly in Syria and Lebanon, with some also in Jordan and Israel. Those in Druse communities, wherever they may be, generally tend to participate in national civic and political life and often serve in the local military, despite maintaining a distinct culture and religious practices.