Huddled in the depths of military headquarters in Tel Aviv, Israel’s wartime leaders had given the green light to the largest and most politically dangerous attack on Iran in Israeli history. They called the operation “Days of Repentance”.

The attack was set up to punish Iran for an attack on Israel, but was aimed at avoiding the start of a full-scale war between the two foes involving American forces and other countries in the region. The attack steered clear of oil and nuclear facilities that Iran had warned would prompt retaliation, and warnings from U.S. officials appeared to have been heeded.

But the attack marked a dangerous new phase of conflict between Israel and Iran, which began attacking each other directly earlier this year. This has left Iran even more vulnerable to new air strikes, with Israel destroying many of the country’s Russian-made S-300 batteries, according to an Israeli official.

“The message is that we do not want to escalate tensions, but if Iran decides to escalate tensions and attack Israel again, that means we are expanding our freedom of movement in Iranian skies,” an Israeli official said.

Israeli Prime Minister Benjamin Netanyahu had been signaling for weeks that Israel would retaliate against Iran’s ballistic missile attack on Israeli territory on October 1. Achieving this required weeks of planning and delicate diplomacy.

Retired Israeli brigadier general Assaf Orion said Iran “knew Israel would come, but they still couldn’t prevent anything.”

Sensing an opening after Israel’s killing of Hamas leader Yahya Sinwar, the United States is pushing for a ceasefire in Gaza. Secretary of State Antony Blinken visited Israel and other Middle Eastern capitals this week in an effort to reach a deal that negotiators had eluded for months. The calibrated nature of the attack appeared to allow those talks to continue, as negotiators met in Qatar’s capital Doha on Sunday.

But while Israel was working on diplomatic channels that could end the war in Gaza and reduce tensions with Tehran, Israeli officials were finalizing details of the retaliatory attack.

On Friday evening, as the sun was setting, symbolizing the beginning of Shabbat, the Jewish day of rest, the Israeli cabinet agreed in a phone call led by Netanyahu to carry out an attack that night, according to an Israeli official.

According to sources familiar with the matter, Israel warned the United States, the Arab world and European capitals about the nature and scope of the attack hours before the attack began. Officials in some of these countries later warned Iran.

The Israeli prime minister’s office later said that the idea that he had informed Iran about the nature or timing of the attack was “false and absurd”.

When they finally started, the Israeli attacks began in waves. People familiar with the mission said the strike involved F-35 fighter jets, Israel’s most advanced air weapon and adept at evading radar.

While the jet fighters were in the air, Israeli officials, aware that their US counterparts were disappointed that Israel had not given advance warning that it would kill Hezbollah leader Hassan Nasrallah last month, also made a point of actively informing their US counterparts about their strikes.

Israeli Defense Minister Yoav Gallant called his US counterpart, Defense Minister Lloyd Austin, and assured him that America was ready to defend Israel against any backlash from Iran and militant groups.

The first jet fighters destroyed air defense batteries in Syria and Iraq, clearing the flight path for the second and third sorties to reach Iran.

The exact route, which was not shared by Israel, was revealed to be to bypass airspace in Jordan after the Arab country said it would not be part of an attack on Iran. Amir Aviv, a former senior Israeli military official who frequently receives briefings from the defense establishment, said most of the attacks were carried out from outside Iranian airspace. Iran said Israeli planes attacked from Iraqi airspace, about 70 miles from its border.

At around 3:30 a.m. in Israel, the Israeli army launched the second of at least three waves of attacks, according to sources familiar with the matter.

Israeli strikes have targeted Iranian facilities involved in the production of missiles such as cruise and ballistic missiles that have targeted Israel twice this year.

One of Israel’s strikes took place at the vast Parchin military facility, where Iran once worked on nuclear weapons capabilities, according to the U.N. atomic agency. Fabian Hinz, a research fellow at the International Institute for Strategic Studies, who focuses on Iran’s missile program, said four buildings were hit there, including three solid-fuel missile facilities.

Just before sunrise, the Israeli army announced that the attack and retaliation had been completed. The planes returned without loss after the 4-hour attack.

Shortly thereafter, Iranian officials began telling Arab countries specifically that the attack had hit the areas with great accuracy. The regime has publicly said this caused “limited damage” and that Iran reserves the right to respond at a time of its choosing. Iran said four Iranian soldiers were killed in the attacks.

Israeli officials said they hoped the attack would end a tit-for-tat conflict with Iran and that the Israeli military could now focus on combat objectives in Gaza against Hamas and Iran’s ally Lebanon’s Hezbollah.

Retired Brigadier General Orion said that the attack was calibrated but did not mean that tensions with Iran were over. “This allows both parties to finish the job for now until the US elections and then see where it goes,” he added.

Anat Peled, Summer Said, Aresu Eqbali and Laurence Norman contributed to this article.