Nel will be replaced by Dale Steyn or Makhaya Ntini, who has had a cortisone injection in his knee and faces a test to decide if he can rejoin the tour.
The first came through West Ham midfielder Jack Collison who started after passing a late fitness test on a knee injury.
For Stoudemire, who has a history of knee problems, the biggest test now will be to build on his health and performance.
Simon Jones wrenched almost every ligament in his knee fielding in the first Ashes Test in November 2002.
Gough may not play every match because of the knee problem that saw him retire from Test cricket last year, but Flower still expects him to make an impact.
The Glamorgan paceman damaged the cruciate ligament in his right knee when fielding last winter in the first Test against Australia in Brisbane.
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Giteau has shaken off a virus that caused him to miss the second Test against Scotland while Gerrard's knee injury has cleared up.
The England Cricket Board said that Pietersen first felt some pain in the knee during fielding practice before the start of the Test series this month, confirming speculation that he had not been completely healthy at the beginning of the tour.
Flintoff is battling an ongoing knee injury that has forced him to announce his retirement from Test cricket at the end of the Ashes series.
With a "pay for performance" plan, a doctor would receive a fixed rate for, say, fixing someone's knee, eliminating the incentive to order up lots of unnecessary test.
The all-rounder, who will retire from Tests at the end of this series because of an ongoing knee injury, took 5-92 in his final Lord's Test on Monday.
Rees has only had two full appearances since returning from a knee injury but the England management are confident he is ready for a Test match return if Worsley is sidelined.
The other main contender for a Test place, Martyn Williams, looked to be struggling with a knee problem.
James Anderson's knee would benefit from another couple of days rest and while Paul Collingwood needs a fitness test before the match, the turn of speed he showed when the rain hit the ground during his gentle loosener looked promising.
"He's been doing some running on the field in straight lines, but when you've got a knee injury it's twisting and turning that causes aggravation and I think he needs to test it in the county game first, " he added.
BBC: SPORT | Cricket | England | Vaughan cools England return talk
Kevin Pietersen will miss out on the Indian Premier League and England's final Test against New Zealand, which begins Friday at Auckland, because of an injury to his right knee.
Ryan Harris's match in Adelaide may have been his first for nine months because of a knee injury but still managed to top the country's bowling statistics before suffering a broken ankle during the fourth Test in Melbourne.
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