Pietersen will fly home tonight after being ruled out of cricket to six to eight weeks with a knee injury that has plagued him since his side's warm-up match in Queenstown earlier in the tour.
The mercurial batsman, who scored 85 runs from three innings after sustaining the injury, will be replaced by Jonny Bairstow for the ANZ series decider, starting at Eden Park tomorrow.
With the injury allowing Pietersen to play the first two tests, questions were raised about whether he would have held on for another five days of cricket if the magnitude of the match justified such an effort.
England will want Pietersen fit for a heavy programme later in the year, including two series against Australia, but captain Alastair Cook said the 32-year-old would have still been on the sidelines tomorrow even if the Ashes were being decided.
"We felt he could get through [the first] two games, but this game might have been a step too far," Cook said. "It's important now we don't jump to too many conclusions. He'll go home, see the specialist and see what's wrong with him.
"It's clearly a very important game. To win any series against any nation away from home is a great achievement. So we've got five days of very tough cricket and we want to finish the winter as well as we can. Clearly you want your best players available."
Pietersen's commitment to the English cause has previously come into question, most recently when he was dropped during last year's tour of his native South Africa after allegedly sending members of the home side text messages in which he was critical of the England set-up.
But Cook defended Pietersen and insisted he had already proven himself during the draws in Dunedin and Wellington.
"With the injury, he hasn't been 100 per cent fit totally. But he's put his body on the line trying to play for England, and that's all you want from all your players.
"I think he's played through a bit of pain for those first two games. He hasn't been 100 per cent fit. But there's got to be a time when you try to manage the situation as well as you can."
Part of that management could see Pietersen back in the lineup when the Black Caps visit England in May. In the meantime, Jonny Bairstow will slot in at No 6 tomorrow while Ian Bell and Joe Root will be shifted one place up the order.
Bairstow last played in the Twenty20 series in February and the last of his five tests came in Mumbai in November, but Cook was backing the 23-year-old to make the most of his opportunity.
"Obviously it's a blow when you lose one of your senior batters and a guy that's performed consistently well for us over a number of years," Cook said. "But it gives an opportunity to Jonny Bairstow coming in. He's probably been a little bit unlucky not to be selected earlier, so he's got a great opportunity to try to end this winter well.
"In an ideal situation, you'd want a little bit more match practice behind you. But sometimes you can't choose that. I know he's just very excited about being given the opportunity."