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The 31-year-old has played 127 ODIs and 36 T20Is and was a first-choice player in both formats.
But he will now continue his England career as a Test specialist only following discussions with the England and Wales Cricket Board earlier this month.
Pietersen said: 'After a great deal of thought and deliberation, I am today announcing my retirement from international one-day cricket.
'With the intensity of the international schedule and the increasing demands on my body, approaching 32, I think it is the right time to step aside and let the next generation of players come through to gain experience for the ICC World Cup in 2015.'
Pietersen, who was man of the tournament when England won the World Twenty20 in the West Indies in 2010, was willing to help defend the trophy in Sri Lanka this autumn.
'I am immensely proud of my achievements in the one-day game, and still wish to be considered for selection for England in Test cricket,' he added.
'For the record, were the selection criteria not in place, I would have readily played for England in the upcoming ICC World Twenty20.'
'For the record, were the selection criteria not in place, I would have readily played for England in the upcoming ICC World Twenty20.'
Best foot forward: KP will now focus on the Test form of the game
Pietersen's absence for the World Twenty20 is particularly relevant given he was the only England batsman to be selected in the recently concluded Indian Premier League.
As a result of his decision, Pietersen's current England contract will be downgraded for the rest of its duration and he will only be available in the future for a lower-tier deal.
The ECB's decision not to allow players to pick and choose between ODI and Twenty20 formats has not previously been made public.
Andrew Strauss was the last senior player to retire from ODI cricket and he was not part of the Twenty20 set-up. As such, today's news brought out an explanation from the board.
Pedigree: Pietersen was player of the tournament at the 2010 World Twenty20 Cup
A statement read: 'The terms of the central contract state that any player making himself unavailable for either of the one-day formats automatically rules himself out of consideration for both formats of the game as planning for both formats is closely linked.
'This is designed to reflect the importance of one-day international cricket which is a strategic priority as England look for improved performances in the 2013 ICC Champions Trophy and the 2015 ICC Cricket World Cup.'
Unclear: KP will likely continue to play in the IPL
Hugh Morris, managing director of England cricket, placed on record his thanks for Pietersen's efforts since his debut in 2004 but did not hide his frustration at the timing.
Morris said: 'The ECB is disappointed by the timing of Kevin's decision less than four months before we defend our ICC World Twenty20 title. Kevin is a world-class player and I would like to take this opportunity to thank him for his efforts and we look forward to his continued contributions to the Test match side.
'The selectors will now replace Kevin in both the ODI and the T20 squads.'
His overall record - nine hundreds and 4184 runs at 41.84 - does not quite do justice to an exceptional talent who announced himself with three centuries in his second one-day series against a hostile South Africa.
KEVIN PIETERSEN FACTFILE
1980: Born June 27 in Pietermaritzburg, South Africa, to an Afrikaans father and an English mother.
1997-98: Makes first-class debut for Natal as an off-spinning all-rounder.
2001: Joins Nottinghamshire with a view to qualifying as an England player, having become frustrated with the quota selection system in South Africa.
2003: Averages more than 50 for the third season running but becomes disenchanted with his county employers and threatens to sue for unfair dismissal, even though relegated Nottinghamshire insist he has not been sacked.
2003-04: Stars for England A in Malaysia and India.
2004
Remains a Nottinghamshire player and helps his team return to the top flight of the County Championship at the first attempt.
September - Selected for the troubled one-day international tour of Zimbabwe even though his qualification period for eligibility is not complete until October.
October - Before travelling to Namibia and Zimbabwe, quits Nottinghamshire for Hampshire.
2005
January - Joins the England squad for the ODI series against his native South Africa.
February - Registers maiden, unbeaten century with 108 in the second match in Bloemfontein. Scores further centuries in East London and Centurion.
Becomes the fastest man in history to reach 500 one-day international runs.
May - Overlooked for Test series against Bangladesh, but named in England's 25-man development squad and one-day squad.
July 14 - Named in England Test squad ahead of Graham Thorpe.
July 24 - Scores 57 and 64 on debut but Australia crush England by 239 runs.
August 7 - Contributes 71 off 76 balls in the first innings as England win by two runs in the second Test at Edgbaston.
September 12 - Scores century to rescue England, who claim the Ashes with a draw in the final Test at The Oval.
2006
March - Fined 30 per cent of his match fee for dissent after a dismissal in the first Test against India. Equals Viv Richards' record of 21 innings to reach 1,000 ODI runs.
May - Becomes the first batsman since 1990 to score a century in three successive Test innings on English soil with 142 against Sri Lanka.
2007
January - England's best player in the 2006-07 Ashes in Australia, scoring 490 runs and averaging over 50.
April - Scores 104 off 122 against Australia, the first World Cup century by an Englishman since 1996. In England's final match against the West Indies, Pietersen makes 100 from 91.
May - Posts his highest score of 226 in the second Test against the West Indies at Headingley.
2008
June - Uses the innovative 'switch hit' in the ODI series against New Zealand - smashing Scott Styris for two sixes. Appointed temporary ODI captain after Paul Collingwood is suspended for four matches.
August 3 - Replaces Michael Vaughan as Test captain and Collingwood as one-day skipper.
August 8 - Scores century in debut innings as Test captain.
September 3 - Captains England to a 4-0 thrashing of South African in the one-day series.
2009
January 1 - Reports of a rift between Pietersen and coach Peter Moores surface.
January 7 - Resigns as England captain.
February - Royal Bangalore Challengers pay a record 1.5m US dollars for Pietersen's services in the IPL auction.
July 22 - With England leading the Ashes 1-0 after two Tests, Pietersen is ruled out of the remainder of the series because of an Achilles injury.
2010
February-March - Struggles for form, particularly against left-arm spin, on the tour of Bangladesh with just 69 from his first seven innings.
April-May - Enjoys a fine tournament as England win the ICC World Twenty20 in the Caribbean, with an unbeaten 73 against Pakistan and 47 in the final victory over Australia.
June 17 - Announces he will not be renewing his Hampshire contract.
June 22 - Plays his 100th ODI against Australia.
August 11 - Left out of Hampshire's squad for Twenty20 finals day.
August 31 - A post on his Twitter account says that he is to be dropped from England's limited-overs matches against Pakistan and has signed for Surrey.
November 2010-January 2011 - On top form in England's Ashes series win in Australia, with the highlight a career-best 227 in Adelaide.
2011
March 7 - Injury forces him out of England's World Cup campaign.
July - Passes 6,000 Test runs with his third Test double-hundred, against India at Lord's.
2012
May 23 - Fined by the ECB for a Twitter outburst against Sky commentator Nick Knight.
May 31 - Retires from one-day and Twenty20 internationals.
Read more: http://www.dailymail.co.uk/sport/cricket/article-2152637/Kevin-Pietersen-retires-limited-overs-cricket.html#ixzz1wSjj8BFb
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