The 25-year-old all-rounder, who was appointed in April after Pakistan's poor showing at the World Cup, was granted a one-year extension by the PCB.
"Malik has shown enough promise to warrant more time as captain," PCB chairman Dr Nasim Ashraf told reporters.
"He has led the team well and all the players are comfortable with him.
"We are looking to have continuity in the captaincy as this is instrumental in the improvement of the team. Malik is young and learning and the perfect choice," he added.
Malik, who is leading the team on its tour of India, has appeared in 20 Tests and 147 one-day internationals for the national side.
Ashraf said the vice-captain would be announced on a series- to-series basis. Younis Khan is the vice-captain for the Indian tour.
Ashraf added that paceman Mohammad Asif might be sent to Australia for treatment on the elbow injury which forced him out of the Indian tour.
"We have two reports on his injury. One specialist says he requires surgery, another feels he can recover without surgery. We have sent his reports to a top specialist in Australia and we are awaiting his response," Ashraf added.
Asif also missed four of the five one-day matches at home against South Africa last month and pulled out of the Indian tour on the day the team left for New Delhi.