17-year-old Md Israfil and 15-year-old Robeya Khatun were married about eight months ago
The operation began at Nabada Housing Society around 12:45am on Wednesday.
DMP Deputy Commissioner Biplab Kumar Sarker said they were searching for suspected militants in the flats where groups of people, usually youths, share rooms.
No-one has been held, he said.
Security forces have strengthened anti-militant drives since the terror attacks in Gulshan and Sholakia earlier in July.
A hideout of militants, suspected to be used by the Gulshan cafe attackers, was recently found at Shewrhaparha in Mirpur.
The youths killed in Kalyanpur had rented the flat and used it as a hideout, police said.