The security forces also took the couple's two young daughters into custody during the raid in the Chaghi district.
"An important al Qaeda commander - Umar Lateef, a Pakistani national - was killed in an encounter with local security agencies," Bugti told reporters.
Umar Lateef had established an al Qaeda network and was supervising its "terrorist activities and providing travel and logistical facilities to terrorists in both Balochistan and south Punjab as well as in Afghanistan," he added.
Read: FC raid: TTP Sajna group members held in Quetta
Bugti said Punjab had offered a reward of Rs2 million for Lateef and half a million rupees for his wife, who was head of al Qaeda's women's wing in south Punjab and Baluchistan.
His wife is being interrogated by security officials.
Al Qaeda announced last September it was setting up a chapter in the sub-continent to counter the spread of the rival Islamic State group, which controls a broad swathe of territory in Iraq and Syria.
Security forces launched a major military operation against Taliban and al Qaeda-led militants in FATA in June 2014.
Read: Rekindling ties: Top al Qaeda operatives captured from Quetta
The operation was intensified in December after Taliban militants attacked a school in Peshawar and killed more than 150 people, mostly schoolchildren.
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