England had made two changes to their side with Eoin Morgan, who deputised as captain in Tuesday's five-run loss, ruled out with a broken right finger.
An England and Wales Cricket Board spokesperson confirmed to Press Association that Morgan would undergo an operation tomorrow on the problem, although a timeframe for his recovery is not yet known.
Morgan suffered the injury during the Champions Trophy semi-final against South Africa on June 19 and had attempted to play through the pain.
His place was filled by Pietersen, with spinner Danny Briggs preferred ahead of Chris Woakes.
New Zealand named an unchanged side but it mattered not as they headed home with a Twenty20 success to go with the 2-1 one-day international series win they secured earlier this month.