Captain Syed Nadeem Naqvi and his wife were attacked by the motorcycle-borne gunmen at Rahmatullah Road near Karachi Stadium.
Both were rushed to a nearby hospital where Naqvi succumbed to his injuries.
Footage on television showed Naqvi's bullet-riddled red Suzuki car.
No group claimed responsibility for the attack though such incidents are usually blamed on the banned Pakistani Taliban and Lashkar-e-Jhangvi.
The incident coincided with Prime Minister Nawaz Sharif's visit to Karachi for a special meeting meeting of his cabinet to frame a strategy to end the cycle of violence that has plagued Pakistan's business hub.
Commander S Azeem Haider Kazmi died of gunshot wounds sustained in an attack in February while Lieutenant Commander Syed Asif Hussain Kazmi and his wife were seriously injured when an improvised explosive device went off under his car within the PNS Karsaz base the same month.
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