"Pietersen experienced knee pain while fielding in preparation for the four-day game in Queenstown earlier this month, ahead of the Test series," an ECB statement read. "This has failed to resolve satisfactorily.
"Recent scans confirm an injury to the right knee with bone bruising and possible cartilage damage to the kneecap. The 32-year-old will return to the UK for further investigations and specialist review.
"The injury is likely to require ongoing assessments and a six-to-eight week period of rest and rehabilitation."
The batsman had been managing the injury throughout the series, and had spent most of a day off the field in the first Test after landing on it awkardly.
The 32-year-old did play in the second Test, scoring 73.
The IPL, where Kevin Pietersen was due to represent the Delhi Daredevils for at least part of the season, runs from April 3 - May 26.
It means that Pietersen has a window of around two months to recover before the first Test of the English summer against New Zealand, scheduled to start at Lord's on May 16.
For the final Test it is expected that Jonny Bairstow will come into the reckoning for Pietersen's place, although the middle order batting positions could be shuffled around.
There was good news for the tourists, however, ahead of the deciding Test in Auckland as James Anderson indicated he would be fit to play.