But England are scheduled to return to South Africa on 1 November for a lengthy tour that comprises two Twenty20 fixtures, five one-day internationals and four Test matches.
Pietersen is desperate to be fit for the tour but he suffered an infection to the scar tissue in his Achilles in mid-August and it seems that the complication has not cleared.
He was operated on initially in late July after his movement became increasingly restricted through the first two Ashes Tests.
The injury first surfaced on England's tour of West Indies in March.
However, Pietersen's recovery was slowed when he strained the tendon again while playing for the Bangalore Royal Challengers in the Indian Premier League in April.
The Hampshire right-hander then missed the one-day series when West Indies made a return visit in May.
Despite clearly struggling at the crease, he averaged 38.25 from four innings at Cardiff and Lord's in the Ashes series, only Jonathan Trott and Andrew Strauss averaging higher among England's players.
The ECB originally estimated Pietersen would be absent for six weeks and he was named in England's initial 30-man squad for the Champions Trophy, but not in the final 15-man party.
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