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The Israeli military declined to comment on the strike, but four Israeli officials, speaking on condition of anonymity to discuss sensitive intelligence matters, acknowledged that Israel had carried out the attack.

The covert war has previously included Israel’s targeted assassinations of Iranian military leaders and nuclear scientists, and Iran’s use of foreign proxies to strike Israeli interests. Now it is increasingly being fought out in open as tensions between the countries have intensified since Israel and Hamas, an Iranian-backed militia in the Gaza Strip, went to war in October.

The attack in Damascus killed Mohamad Reza Zahedi, 65, a senior commander in the Quds Force. General Zahedi, Iranian officials said, oversaw the Quds Force’s covert military operations in Syria and Lebanon.

Also killed in the strike were Gen. Mohammad Hadi Haj Rahimi, a deputy commander of Quds Forces in Lebanon and Syria and second in command to General Zahedi, and Gen. Hossein Aman Allahi, responsible for the Quds Force’s military operations in the region, according to Iranian media and an official statement from the Guards.

“For years, Israel and Iran have been engaged in what’s usually called a ‘shadow war,’” Ali Vaez, the Iran director for the International Crisis Group, said Monday in a social media post. “Today’s strike underscores the fact that this is increasingly a misnomer, as tensions increase on multiple fronts.”

Nasser Kanaani, the spokesman for Iran’s foreign ministry, said Iran was still investigating the scope of the attack but threatened that there would be consequences for Israel. “Iran, in addition to having the right to retaliate in kind,” Mr. Kanaani said, “will decide on how to respond and punish the aggressor.”

Syrian and Iranian state news agencies reported that at least seven people were killed in the strikes on Monday and aired video footage of the ruined building, the remnants of burned cars, shattered glass and debris covering the ground.

The strike, two members of Iran’s Revolutionary Guards said, targeted a secret meeting in which Iranian intelligence officials and Palestinian militants gathered to discuss the war in Gaza. Among them were leaders of Palestinian Islamic Jihad, a group armed and funded by Iran.

Israel and Iran differed in their descriptions of the building that was hit. Iran described it as part of its diplomatic mission in Syria, but Israel said it was being used by the Revolutionary Guards, making it a legitimate military target.

“This is no consulate and this is no embassy,” the Israeli military spokesman, Rear Adm. Daniel Hagari, told CNN. “This is a military building of Quds Forces disguised as a civilian building in Damascus.”

Mr. Vaez, the analyst, said, “Targeting a diplomatic facility is akin to targeting Iran on its own soil.” Failure to retaliate would undermine Iran’s military presence in Syria, he said, but “If they do respond they would fall into the trap that they think Israel has laid for them to get into a direct war.”

Iran’s foreign minister, Hossein Amir Abdollahian, strongly condemned the attack in a statement and said he had spoken to his Syrian counterpart about the “Zionist regime’s attack on the consulate section of the Islamic Republic’s embassy in Damascus.”

Syria’s defense ministry said the strikes happened around 5 p.m. local time when Israeli fighter jets entered Syria from the Golan Heights.

Iran’s ambassador to Syria, Hossein Akbari, said in a statement released to state media that the consulate’s building came under attack by two F-35 fighter jets. Mr. Akbari said among those killed were several Iranian military advisers deployed to Syria.

“This attack will have our fierce response,” he said, according to Iranian media.

The attack rattled supporters of Iran’s government who took to social media to question, once again, how Israel knew of the secret meeting and whether Iran’s security apparatus had been infiltrated by informants.

Peyman Syed Taheri, a conservative analyst close to the government, said in an interview from Tehran that Israel’s attack in Damascus had shaken Iranians who fear that the government’s approach to the standoff with Israel had failed.

“Our national security has been violated. Either Iran must respond so Israel doesn’t attack us in Tehran or if it doesn’t want to respond then it has to rethink and moderate its regional policies and military presence,” Mr. Taheri said.