Pietersen himself said after the Scotland match, that the Injury was not a problem, and that the fact he was even diving around in the outfield was a sign that he was well on the road to recovery.
His place is taken by Kent captain Rob Key, who will bat at number 3.
In another surprise move, England have opted for Adil Rashid ahead of Graeme Swann for the curtain opener at Lord's.
It is rumoured a back injury has accounted for Swann's absence.
Play starts at 17.30.
England: Wright, Bopara, Key, Shah, Collingwood, Morgan, Foster, Rashid, Broad, Sidebottom, Anderson,
England medical officer Nick Peirce told the BBC on the subject of Kevin Pietersen "Kevin had been making excellent progress with the management of his right Achilles injury and had shown substantial improvement. However today he has experienced a degree of pain which medical assessments have suggested may be related to some aggravation from his lower back.
"In order to continue maximising his recovery for the remainder of the tournament and the summer ahead, he will undergo a scan and an injection today.
"Provided this injection has the expected result Kevin may well be available for selection for England's match against Pakistan on Sunday. He will continue to be assessed and receive treatment over the next 48 hours before a decision is made."
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