New Zealand, chasing 288 for victory, finished on 253 all out but still took the series 2-1 after five-wicket and 86-run wins at Lord's and Southampton respectively.
Ross Taylor top-scored with 71 for the Black Caps while recalled England off-spinner James Tredwell took three for 51.
Earlier, England made 287 for six with Ian Bell top-scoring with 82 and Jos Buttler's 47 not out taking just 16 balls.
This was both sides' final match before the one-day Champions Trophy tournament in the UK starts on Thursday.
<Center><b><i>Copyright AFP (Agence France-Presse), 2013</b></i></center>