In his absence, Mohammad Rizwan will lead the side.
“Babar had a full-fledge training session yesterday but felt slight pain in his thumb, following which, the team management has opted against taking any risk,” read the PCB statement.
Babar had to sit out the three-T20I series and the first Test, at Mount Maunganui, after he fractured his right thumb during a net session in the lead-up to the white-ball series.
Sharing details on the injury, Team Doctor Dr Sohail Saleem said: “We have seen improvement in Babar Azam’s injury but he is yet to fully recover. He is our captain and the most important batsman in the lineup, so we do not want to take any risk.
“The medical team is constantly reviewing his injury and we are hopeful he will be available for the home series against South Africa.”
New Zealand is currently leading the two-match series 1-0.