The batsman was included in the 50-over party for the five-match series in India next month after his successful 'reintegration' into the national set-up, but will not head to New Zealand as selectors look to manage the workload of key players.
James Anderson, Jonathan Trott and Graeme Swann have returned to the 14-man one-day squad after being rested for the India series.
The 14-man T20 squad features two changes from the party selected for the recent series against India with Stuart Broad returning from a heel injury to captain the side and quick Steven Finn also back in the fold.
National selector Geoff Miller said: "Following on from the ODI tour to India the tour to New Zealand will require players to adapt to different conditions and will prove a real challenge for the squad as we look to continue the progress we have made in limited overs cricket recently.
"There are a number of players who we have decided not to select for parts of the competitive programme this winter as we look to manage their workloads effectively while ensuring we remain competitive across all formats.
"We feel this is the best way of keeping players as physically and mentally fresh as possible during a demanding 2013 and beyond.
"Kevin Pietersen will miss the limited overs tour of New Zealand with Graeme Swann missing the T20 leg of the tour.
"This approach also provides an opportunity for talented young players to gain more international experience which will be important for their development and the development of England sides in the future."
England's three-match ODI series begins on February 17 in Hamilton.