Sinwar is believed to remain in hiding in Gaza.
Israel has not confirmed or denied it was behind Tuesday’s strike in Tehran that killed Ismail Haniyeh, Hamas’ political chief.
Hamas has said Deif survived the July attack in Gaza and did not immediately comment on the military’s announcement of confirmation.
The killing of two of Hamas’ most senior figures brings a victory for Israeli Prime Minister Netanyahu, who has said that he will not end the campaign in Gaza until Israel destroys Hamas’ military capabilities.
Israeli Defense Minister Yoav Gallant said the strike that killed Deif was a “significant milestone” toward achieving the goals of the war.
“The results of this operation reflect that Hamas is an organisation in disintegration,” he wrote on X.
Israel targeted Deif in a July 13 strike that hit a compound on the outskirts of the southern Gaza city of Khan Younis.
The military said at the time that another Hamas commander, Rafa Salama, was killed.
More than 90 other people, including displaced civilians in nearby tents, were killed in the strike, Gaza health officials said at the time.
In a statement on Thursday, the Israeli military said that “following an intelligence assessment, it can be confirmed that Mohammed Deif was eliminated in the strike.”
Civilians flee in Rafah as Israel pushes ahead with its offensive
In its 10-month-old campaign of bombardment and offensives in Gaza, Israel has killed some 39,480 Palestinians and wounded more than 91,100 others, according to Gaza’s Health Ministry, whose count does not differentiate between civilians and combatants.
More than 80 per cent of the population of 2.3 million have been driven from their homes, the vast majority crammed into tent camps in the southwest corner of the territory, with limited food and water.
Deif was one of the founders of Hamas’ military wing, the Qassam Brigades, in the 1990s and led the unit for decades.
Under his command, it carried out dozens of suicide bombings against Israelis on buses and at cafes and built up a formidable arsenal of rockets that could strike deep into Israel and often did.
He remained a mysterious, underground figure in Gaza. He never appeared in public, was hardly ever photographed and only rarely was his voice heard in audio statements. He survived a string of Israeli assassination attempts.