"Tamim Chowdhury is dead," said senior police officer Sanwar Hossain, referring to the Bangladeshi-Canadian suspected mastermind.
Two other suspected militants were killed by police during the raid.
The cafe attack began on 1 July when the militants entered the Holey Artisan Bakery in Dhaka.
They held hostages for 12 hours before police stormed the cafe, rescuing 13, killing six gunmen and arresting another.
Twenty hostages and two police officers were killed in the attack, the worst in the country's history.
