Whiteley suffered a groin injury in training and is replaced by Sikhumbuzo Notshe, who will makes his first start for the Springboks.
Cheslin Kolbe is also in the starting XV for the first time, selected at right wing, which allows Jesse Kriel to move to centre alongside Andre Esterhuizen.
The midfield pairing has been changed after Lukhanyo Am fractured his forearm and Damian de Allende was also injured in South Africa’s upset 36-34 win over world champions New Zealand in Wellington.
Kolbe, based at French club Toulouse, won a unexpected call-up for the tests in Australia and New Zealand and scored a try against the All Blacks.
“Cheslin has been very impressive since he joined the squad a few weeks ago and now he gets a deserved opportunity to start in a big test,” coach Rassie Erasmus said on Thursday.
“The same applies for Notshe, who did very well in the role of impact player during the English series. He has kept on working hard and he deserves his opportunity in the starting team.”
Tendai Mtawarira return to first-choice loosehead prop with Steven Kitshoff dropping to the bench.
South Africa will be looking to build on the momentum of the win over the All Blacks and keep alive their chances of winning this year's southern hemisphere championship.
Team:
15-Willie le Roux, 14-Cheslin Kolbe, 13-Jesse Kriel, 12- Andre Esterhuizen, 11-Aphiwe Dyantyi, 10-Handre Pollard, 9-Faf de Klerk, 8-Sikhumbuzo Notshe, 7-Pieter-Steph du Toit, 6-Siya Kolisi (captain), 5-Franco Mostert, 4-Eben Etzebeth, 3-Frans Malherbe, 2-Malcolm Marx, 1-Tendai Mtawarira
Replacements: 16-Bongi Mbonambi, 17-Steven Kitshoff, 18-Wilco Louw, 19-RG Snyman, 20-Marco van Staden, 21-Embrose Papier, 22-Elton Jantjies, 23-Damian Willemse.
(Reporting by Mark Gleeson; Editing by Ed Osmond)
