His wife sustained injuries in the attack and has been admitted hospital.
Prime Minister Nawaz Sharif expressed extended his condolences to the bereaved family and directed law enforcement agencies to beef up security in Karachi.
"Ongoing military operation in Karachi against militants and criminals would continue with full force till their complete elimination," said PM Sharif.
The shootout was reported after 43 persons of Ismaili community were killed on Wednesday when gunmen opened fire on a bus in which they were travelling in.
Jundullah, a splinter group of the Tehreek-i-Taliban Pakistan (TTP) later claimed responsibility for the bus attack on Ismaili community.
Karachi, the largest metropolitan city of Pakistan, is riddled with targeted killings, gang wars, kidnappings for ransom, extortion and terrorism.