Last week the 32-year-old was dropped for the third and final test against South Africa at Lord's after having sent "provocative" text messages about his own team mates and management to opposition players.
England slipped to a 51-run defeat to lose the series 2-0 and concede the number one test ranking to South Africa.
"Kevin Pietersen's future involvement is still being determined and he was therefore not considered," national selector Geoff Miller said.
The party to face South Africa in five one-day internationals starting in Cardiff on Friday also sees Twenty20 captain Stuart Broad rested ahead of next month's World Cup in Sri Lanka.
"Stuart has an important period coming up leading our T20 side and ... we feel a two-week break from cricket is in the best interests of both him and the team," said Miller.
Pietersen could have been selected for both squads, having reversed a decision he made in May to retire from all forms of international limited-over cricket.
The South African-born batsman was one of the key players when England won the Twenty20 World Cup two years ago.
England coach Andy Flower described the Pietersen issue as "a very sad situation for everyone involved".
"He played superbly at the last Twenty20 World Cup but the circumstances that exist at the moment mean he can't be selected," Flower told Sky Sports.
"There are still unresolved issues and we will be addressing those when we have time to do so."
Echoing the comments made by England test captain Andrew Strauss last week, Flower said there were issues of "trust and mutual respect" that had to be sorted out.
"Let me be clear, this is not just an issue between the captain and Kevin," he added.
"There are unresolved issues that have reared their heads in recent weeks and they have to be resolved before there is any way forward.
"You resolve these issues face-to-face with people. Andrew Strauss and I have worked very closely and very well together over the years and we will continue to do so over this issue.
"Andrew is a superb leader and he can certainly take this side on. He deserves a little break and he's taking it now," said Flower.
"He'll come back feeling refreshed, I'm sure."
Full England squad: Stuart Broad (captain), Jonny Bairstow, Ravi Bopara, Tim Bresnan, Danny Briggs, Jos Buttler, Jade Dernbach, Steven Finn, Alex Hales, Craig Kieswetter, Michael Lumb, Eoin Morgan, Samit Patel, Graeme Swann, Luke Wright.