Only two balls had been bowled, with England two for one, when rain stopped play after Michael Lumb was caught at second slip by New Zealand captain Brendon McCullum off left-arm quick Mitchell McClenaghan.
Rain prevented all further attempts at a re-start, with officials seeing plans for a six-overs-per-side match starting at 9.03pm local time (2003GMT) thwarted by a fresh downpour.
The no-result, in what was the final match of their tour, gave New Zealand the two-match series 1-0 after their five-run win at The Oval on Tuesday and followed their 2-1 one-day series success.
However, England took the preceding Test series 2-0.
England made two changes from the side that lost the first of this two-match series by five runs at The Oval on Tuesday.
Pietersen was included in an England side for the first time following a knee injury that forced his early exit from the tour of New Zealand in March.
The former England captain was sidelined from all cricket until making a superb unbeaten 177 for Surrey in a County Championship match last weekend.
But he took no active part Thursday and will now turn his attention to England's Ashes four-day warm-up match against Essex at Chelmsford starting on Sunday.
England begin the defence of the Ashes against Australia with the first Test at Trent Bridge on July 10.
South Africa-born Pietersen, 33 on Thursday, replaced stand-in captain Eoin Morgan, who led England on Tuesday in the absence of the rested Stuart Broad, after the former Ireland international was ruled out with a right hand injury.
Kent off-spinner James Tredwell captained England for the first time but had still to lead the side in the field after losing the toss.
Left-arm spinner Danny Briggs, a key member of English domestic Twenty20 champions Hampshire's side, replaced seamer Chris Woakes, whose one over on Tuesday cost 19 runs.
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