Rizwan and Irfan both suffered hamstring injuries in the third match in Rawalpindi, where a second-string New Zealand side won by seven wickets to level the five-match series 1-1
Kohli remained unbeaten on 254 for his highest score in his 50th Test as skipper.
It was his first Test hundred of the year and 26th of his career.
The hosts lead the three-Test series 1-0 after their win in the opener at Visakhapatnam.