X-rays showed no serious injury and he made himself available for selection as a batsman only, but the selectors decided not to take any risks.
Explaining the choice to send England into bat, South African captain Temba Bavuma said: “It’s a hard ground to defend, with short straight boundaries.
“It also tends to get easier to bat on under lights.”
Fast bowler Anrich Nortje and left-arm spinner Keshav Maharaj were replaced by Sisanda Magala and Tabraiz Shamsi.
England captain Jos Buttler said he would have preferred to chase.
“We are disappointed to be out of the series but there is lots to play for today,” he said.
Fast bowler Jofra Archer returned in place of Olly Stone.
South Africa: Temba Bavuma (c), Reeza Hendricks, Rassie van der Dussen, Aiden Markram, Heinrich Klaasen (wk), David Miller, Marco Jansen, Wayne Parnell, Sisanda Magala, Lungi Ngidi, Tabraiz Shamsi
England: Jos Buttler (c) (wk), Jason Roy, Dawid Malan, Ben Duckett, Harry Brook, Moeen Ali, Chris Woakes, Sam Curran, Adil Rashid, Jofra Archer, Reece Topley