The IDF and a senior Hamas official confirmed Izz al-Din al-Haddad, who was born in 1970, was killed in the attack on Friday.
Hamas has not publicly announced Haddad's death.
At Al Aqsa Martyrs mosque in central Gaza a joint funeral was held on Saturday for Haddad, his wife and 19-year-old daughter. It was not immediately clear how they died.
Israeli Prime Minister Benjamin Netanyahu said in a joint statement with his defence minister on Friday that Haddad had been targeted, though they did not say if he had been killed.
Netanyahu and Defence Minister Israel Katz said Haddad was an architect of the October 7, 2023 attacks launched by Hamas militants that precipitated Israel's ongoing assault on Gaza.
Haddad, who became the group's military chief in Gaza after Israel's killing of Mohammad Sinwar in May 2025, "was responsible for the murder, abduction, and harm inflicted on thousands of Israeli civilians (and) soldiers," they said.
Nicknamed "the Ghost", Haddad had survived multiple assassination attempts by Israel, according to Hamas sources.
The IDF says he was one of Hamas' longest-serving commanders, rising through the ranks from the group's early establishment in the 1980s to hold several senior positions.
Israel and Hamas remain deadlocked in indirect talks to advance US President Donald Trump's post-war plan for Gaza that is meant to end more than two years of fighting.
Medics in Gaza on Friday said at least seven people, including three women and a child, were killed and at least 50 injured in air strikes targeting an apartment and a vehicle.
Israel has escalated its attacks in Gaza in the weeks since halting its joint bombing with the US in Iran, redirecting its fire back on the ruined Palestinian territory where the military says that Hamas fighters are tightening their grip.
