The 32-year-old - man of the tournament when England won the 2012 World Twenty20 competition - was axed for the final Test against South Africa after admitting sending "provocative" text messages about skipper Andrew Strauss to opposing players.
That made his participation in the three-match NatWest International T20 Series against the tourists and the forthcoming World T20 in Sri Lanka next month unlikely and his omission has been confirmed by the England and Wales Cricket Board.
"Kevin Pietersen's future involvement is still being determined and he was therefore not considered for selection in either squad," said Miller in announcing the squads.
"The T20 squad mirrors the squad we have selected for the ICC World Twenty20 in Sri Lanka and the three-match NatWest series provides this group of players with valuable preparation in what will be a highly-competitive series ahead of the tournament starting in September."
The squad to face South Africa also sees Twenty20 captain Stuart Broad rested ahead of his leadership duties in Sri Lanka.
"Stuart has an important period coming up leading our T20 side and with a three-match series followed closely by the ICC World T20 we feel a two-week break from cricket is in the best interests of both Stuart and the team," explained Miller.
While Broad has been left out of the five-match NatWest ODI Series against the Proteas, Essex all-rounder Ravi Bopara has been given an additional match to improve his sharpness with a guest appearance for Gloucestershire in their match against the tourists.
Luke Wright and Michael Lumb are also named, both making their return to the squad for the first time since June 2011.
The first one-day international is on Friday at Cardiff, followed by matches at the Ageas Bowl in Southampton, the Oval, Lord's and Trent Bridge.
England International T20 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