Last week, the 32-year-old Pietersen was dropped for the third and final Test against South Africa at Lord's after admitting to sending "provocative" text messages to opposing players.
England slipped to a 51-run defeat in the match to lose the series 2-0 and concede the number one Test ranking to their opponents in the process.
National selector Geoff Miller explained Pietersen's international future "was still being determined" so it was always unlikely the England and Wales Cricket Board (ECB) were going to select him for the upcoming limited overs events.
"Kevin Pietersen's future involvement is still being determined and he was therefore not considered for selection in either squad," Miller said as the squads were announced.
The squad to face SA for the five one-day internationals also sees Twenty20 captain Stuart Broad rested ahead the Twenty20 World Cup in Sri Lanka in September and October.
Pietersen could have been selected for both squads, having reversed a decision to retire from all forms of international limited-overs cricket, at which he was one of the key players when England won the last global 20-over event two years ago.
The ODI series starts in Cardiff on Friday and continues with matches at Southampton, the Oval, Lord's and Trent Bridge.
Miller continued: "All players in the 14-man ODI series squad were involved in the recent series victory against Australia.
"We will be looking for this side to build on the recent success we have had and to show further signs of improvement against a strong SA side.
"Stuart Broad has an important period coming up leading our T20 side and with a three-match series followed closely by the (World Cup), we feel a two-week break from cricket is in the best interests of both Stuart and the team."
In Broad's absence Alastair Cook will captain the one-day side. – Reuters