Israel said the attack killed the commander of the Iran-backed group’s elite Radwan force.
Hezbollah, which controls Beirut’s southern suburbs, has yet to issue any statement on the strike or the commander’s status.
“He likely read in the press that he had immunity in Beirut. Well, he read it and it is no longer the case,” Netanyahu said in a statement.
Hostilities between Israel and Hezbollah reignited on March 2 when the group opened fire at Israel after Tehran came under US-Israeli attack.
Wednesday’s strike raises pressure on the Lebanon ceasefire that emerged in parallel to a truce in the wider Middle East war, with a halt to Israeli strikes in Lebanon being a key Iranian demand in Tehran’s negotiations with Washington.
Announced on April 16 by US President Donald Trump, the Lebanon ceasefire has led to a reduction in hostilities: the Beirut area was not struck by Israel for weeks before Wednesday’s attack.
However, the sides have continued to trade blows in the south, where Israel has carved out a self-declared security zone.
Netanyahu said the Hezbollah commander, identified as Ahmed Ali Balout by the Israeli military, “thought he could continue to direct attacks against our forces and our communities from his secret terrorist headquarters in Beirut”.
“I say to our enemies in the clearest possible way: No terrorist has immunity,” he said.
While Israel and Hezbollah wage war, the US has hosted two rounds of talks between the Lebanese and Israeli ambassadors to Washington, the highest-level contacts between Lebanese and Israeli government representatives in decades.
A US state department official said representatives of Israel and Lebanon would hold a third round of talks in Washington on May 14 and 15.
The Lebanon ceasefire was announced for an initial 10 days and then extended for an additional three weeks during the second meeting between the Lebanese and Israeli ambassadors to Washington, hosted by Trump at the Oval Office.
Hezbollah strongly objects to the Lebanese government’s contacts with Israel, which reflect deep differences between the group and its critics in Lebanon.
Lebanese PM says too early for ‘high-level’ meeting
More than 2,700 people have been killed in the war in Lebanon since March 2, Lebanon’s health ministry says.
Some 1.2 million people have been driven from their homes, many of them fleeing from southern Lebanon.
Israel says 17 of its soldiers have been killed in southern Lebanon, along with two civilians in northern Israel.
At least 11 people were killed in Israeli strikes in three different areas of south Lebanon on Wednesday, according to a tally of Lebanese health ministry announcements.
Hezbollah said it carried out 17 operations against Israeli forces in southern Lebanon on Wednesday, while the Israeli military said it had struck more than 15 militant infrastructure sites in the south the same day.
The Israeli military says Hezbollah has fired hundreds of rockets and drones at Israel since March 2.
Hezbollah says it has the right to resist Israeli forces occupying the south.
Israel’s control zone extends as deep as 10km into southern Lebanon. Israel says it aims to protect northern Israel from Hezbollah militants embedded in civilian areas.
Trump said last month he looked forward to hosting Netanyahu and Lebanese President Joseph Aoun in the near future, and that he saw “a great chance” the countries would reach a peace deal this year.
However, on Wednesday, Lebanese Prime Minister Nawaf Salam said it was premature to talk of any high-level meeting between Lebanon and Israel, and said that shoring up a ceasefire would be the basis for any new negotiations between Lebanese and Israeli government envoys in Washington.