Ibrahim Aqil, who had a $7million (£5.2million) reward on his head, was killed in the strike on a meeting of the militant group's elite Radwan force in its stronghold of the southern suburb of Dahieh yesterday.
Israel said its assault also killed 10 other leading Hezbollah figures.
Local health staff said at least 12 people died and more than 60 were injured in the attack - Israel's third on Beirut this year.
Video of the aftermath showed debris and vehicles strewn across a major street as people searched the burning remains of a multi-storey building.
The strike came hours after overnight air raids on Hezbollah targets in Lebanon. The Israel Defence Forces claimed its jets destroyed at least 100 rocket launch sites in what amounted to one of the heaviest bombardments for a year.
The Iran-backed group hit back, firing at least 140 rockets at Israel from Lebanon amid growing fears of total war in the Middle East.
A salvo of 60 flew towards northern Israel yesterday morning, setting off sirens in the Galilee area.
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