Pietersen, 33 today, has not pulled on an England shirt for three months following a knee injury suffered on the tour of New Zealand in March.
Tonight's match represented the right-hander's only chance to face international opposition before the Ashes begin at Trent Bridge on July 10.
He was one of two changes from the England team that lost Tuesday's opener by five runs, with James Tredwell taking over as captain for the first time after Eoin Morgan suffered a broken finger.
Chris Woakes also dropped out to be replaced by spinner Danny Briggs.
New Zealand named an unchanged line-up and skipper Brendon McCullum sent in England after winning the toss under grey skies.