Nurul Islam Marzan and a second unidentified man were killed in the early hours of Friday in Dhaka.
The deaths happened when anti-terrorism police raided a building in the Rayer Bazar area, police told AFP.
The cafe hostages were shot or hacked to death in what was Bangladesh's worst terror attack.
Commandos stormed the Holey Artisan cafe in the Gulshan neighbourhood after a 12-hour siege, rescuing 13 people. Two police officers and six militants were also killed in the 1 July attack.
Police said Marzan was a senior figure in the banned militant group Jamaat-ul Mujahideen Bangladesh (JMB) and was believed to have been the operational commander of the attack.
They say he planned it with Tamim Ahmed Chowdhury, a Canadian of Bangladeshi descent, who was killed in a police raid near Dhaka in August 2016.
There is no independent confirmation of what happened. In August there were accounts suggesting Marzan was being held in police custody, even as the authorities said they were trying to arrest him.
The so-called Islamic State (IS) claimed responsibility for the cafe attack, posting online images of the attackers with a black IS flag. But Bangladeshi authorities have long insisted IS has no presence in the country and that JMB was solely to blame.
Since the attack, authorities have led a crackdown on militants, leaving dozens dead, many of them senior members of JMB.
Police said Marzan, who was about 30, joined a branch of JMB in 2015 after dropping out of Chittagong University, where he was an Arabic student.

The 65-year-old will appear in Belfast Magistrates Court on Monday to be charged with the murders of John Devine in 1989 and John O'Hara in 1991.
John Devine, 37, was shot dead at his home on Fallswater Street in west Belfast on 23 July 1989.
He was sitting in his living room with his 13-year-old son when three men forced their way in and shot him.
John O'Hara, 41, was murdered on Dunluce Avenue in south Belfast on 17 April 1991.
He was working as a taxi driver and had gone to pick up a passenger at 22:15 BST, when he was approached by two masked men who fired several shots at the car, fatally injuring him.
Officers from the Legacy Investigation Branch (LIB) of the PSNI arrested Mr Rea on Tuesday.
Last September the LIB announced that it would re-examine the murders after they gained access to tapes containing interviews Mr Rea gave to the Boston College 'Belfast Project'.
One of the suspected masterminds of the cafe attack in Dhaka, Bangladesh in July in which 20 hostages died has been killed in a shootout, police say.
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Belfast loyalist Winston 'Winkie' Rea has been charged with two counts of murder dating back more than 20 years.