The Test will be played at Lord's and follows the draw at Headingly.
The batsman became the quickest player to reach 7000 Test runs after a sparkling display in that match but left the ground under a cloud of uncertainty having been reluctant to assuage rumours that he would quit international cricket. Pietersen has since intimated that he has had a "change of heart" regarding his international future and would be willing to continue playing for England in all formats of the game, but his exclusion yesterday hinted that the authorities are not inclined to forgive and forget.
He has endured a controversial week – even by his standards – and it seems a final sticking point persisted over the text messages he reportedly sent to South Africa players during the Headingley Test. His place has been filled by Jonny Bairstow.
It emerged he had been perturbed by a parody Twitter account and the possibility that his team-mates – among the followers of a feed since closed down – might somehow be associated with the mocking tone, sending up his personality and behaviour. He then sent texts to South Africa players in a troubling series for England. It is that which appears to be what has truly undermined Pietersen's attempts at reconciliation with England and Wales Cricket Board management.
"To say I am gutted is an understatement," said Pietersen yesterday. "This entire episode has been demoralising for me and my family. But, this is not the end of my international career."
He had made it clear in an earlier interview on YouTube that he had seen the error of his ways and had decided playing cricket for England was more important than other issues. However, after a summer dominated by Pietersen's contract wrangles with the ECB since his surprise retirement from limited-overs international cricket at the end of May, it seems it has all been too little too late to convince the authorities he is a changed man.
"During the past week we have held several discussions with Kevin Pietersen and his advisers," said Hugh Moris, managing director England Cricket. "Following a constructive meeting, it was agreed that a number of actions needed to be completed to re-engage Kevin within the England dressing room.
"A fundamental item was to confirm publicly that no derogatory texts had been sent by Kevin to the South African team. This has not been forthcoming, despite clear timelines being set to allow the selectors to pick the squad for the third Investec Test Match.
"We provided an additional six hours this morning to provide every opportunity for agreement to be reached, but regrettably this has not been possible. While we have made every attempt to find a solution to enable Kevin to be selected, we have sadly had to conclude that he will miss the Lord's Test."
Pietersen's absence means a return for the 22-year-old Yorkshireman Bairstow, dropped after his third Test against West Indies earlier this summer amid concerns he was having trouble handling the short ball at the highest level. Bairstow scored a century for England Lions against Australia A this week. Also in a squad are James Taylor, who shared a century stand with Pietersen last week, seamer Graham Onions and off-spinner Graeme Swann – both of whom were left out of the last Test.