Khan, 56, was appointed after Waqar quit on health grounds in September, and later helped Pakistan win a clean sweep over Sri Lanka and Bangladesh.
"Khan will be the coach for the series against England next month," the Pakistan Cricket Board (PCB) said.
The PCB had formed a three-member committee to find a replacement for Waqar, which shortlisted a few names, including former Sri Lanka coach Dav Whatmore who was invited for an interview next month.
Pakistan plays three Tests, four one-day internationals and three Twenty20s against England in the United Arab Emirates between January 17 and February 27.
Former Test paceman Aaqib Javed was recalled as bowling coach after being dumped in September, while former middle order batsman Ijaz Ahmed was retained as fielding coach.
Naveed Cheema will be manager for the series, the PCB said.
Pakistan on Monday announced a 15-man squad for the three Tests. The first Test starts in Dubai from January 17.(AFP)
