"He will not be at the ground today and will have a second scan to determine the extent of the injury," an ECB statement read on Friday.
Jofra Archer has been ruled out of England's second Test against South Africa through injury.
The seamer is suffering from an elbow problem which prevented him from taking any serious part in training in the immediate build-up to the game at Newlands.
"He (Archer) is not fit to play suffering with a right elbow injury," an ECB statement read.
"He will not be at the ground today and will have a second scan to determine the extent of the injury."
Somerset spinner Dom Bess, who had not been originally included in the touring party but was called up after Jack Leach went down ill, replaces Archer in the England side.
The visitors have made two further changes to the side which lost the opening match of the series at Centurion.
Rory Burns is replaced by Zak Crawley after suffering a series-ending ankle ligament injury playing football on Thursday, while Ollie Pope comes into the middle order in place of Jonny Bairstow.
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