Nurul Islam Marjan, a commander of a splinter group of the Jamaat-ul-Mujahideen Bangladesh (JMB) jihadist group, was killed along with another militant, Monirul Islam, chief of Dhaka's counter-terrorism police said.
Marjan was on a police wanted list for his role in the attack on the cafe last July, which raised alarm over the rising threat of Islamist militancy and cast a shadow over foreign investment in the poor Muslim country.
So far police have hunted down and killed at least 40 militants linked to the cafe attack, including mastermind Tamim Chowdhury.
Police have attributed several attacks over the past two years to JMB, which says it is affiliated to Islamic State although the government insists Islamic State has no presence in Bangladesh.
In September, police arrested Marjan's wife, Shaila Afrin Prioyti, along with other two female militants in Dhaka.
Marjan, who studied Arabic at Chittagong University, had disappeared a year ago from his family's village in Pabna district, 160 km (100 miles) north of the capital, police said.
While the government has dismissed Islamic State's claim of responsibility for the attack on the cafe, security experts say the scale and sophistication of the assault suggested links to trans-national networks.
Investigators are still seeking Syed Mohammad Ziaul Haque, a militant who was an army major before his dismissal from the forces.
Nurul Islam Marjan was killed along with another militant.
Bangladesh counter-terrorism police shot dead two Islamist militants on Friday in a gunfight in Dhaka, including a prime suspect in the slaughter of 20 hostages, mostly foreigners, in an attack on a cafe in the capital last year.
