"Jahangir Badini, the mastermind behind the suicide attack on civil hospital, was killed during the operation," Balochistan Home Minister Mir Sarfaraz Ahmed Bugti said.
"So far three of the five terrorists have been identified," he told reporters.
The militants killed in the operation were involved in a series of terror acts including attack on Hazara women and the murder of Barrister Amanullah Achakzai, the principal of University of Balochistan's law college.
The suicide bomber, who attacked Quetta Civil hospital on August 8, was identified with the help of DNA tests. His name was Ahmed Ali and he was a resident of Quetta, Bugti said.
Tehreek-i-Taliban Pakistan splinter group Jamaat-ul-Ahrar had claimed responsibility for the attack which occurred at the gates of the building housing the emergency ward.
Most of those killed were lawyers who had gathered at the hospital to mourn the death of Balochistan Bar Association chief Advocate Bilal Anwar Kasi who was killed hours before by unknown gunmen.