The loosehead pillar suffers from shoulder pain and was replaced in the starting XV by Rory Sutherland. Mako Vunipola enters the bench.
Jones suffered a shoulder injury against South Africa A 10 days ago but was declared fit for the game.
“It’s really bad luck for Wyn and we all feel he missed tonight’s game,” said Warren Gatland.
“However, we are confident he will be back in training next week and have no plans to bring anyone else in at this point. ”
The Welshman had impressed with his scrum performance in that game as well as his overall contribution on the pitch.
Sutherland, however, was in good shape during the tour.
You can follow the latest preparation and the game live here.
British and Irish Lions: 15. Stuart Hogg, 14. Anthony Watson, 13. Elliot Daly, 12. Robbie Henshaw, 11. Duhan van der Merwe, 10. Dan Biggar, 9. Ali Price, 1. Rory Sutherland, 2. Luke Cowan-Dickie, 3 Tadhg Furlong, 4. Maro Itoje, 5. Alun Wyn Jones (capitaine), 6. Courtney Lawes, 7. Tom Curry, 8. Jack Conan.
Substitutes: 16. Ken Owens, 17. Mako Vunipola, 18. Kyle Sinckler, 19. Tadhg Beirne, 20. Hamish Watson, 21. Conor Murray, 22. Owen Farrell, 23. Liam Williams.
South Africa: 15. Willie le Roux, 14. Cheslin Kolbe, 13. Lukhanyo Am, 12. Damian de Allende, 11. Makazole Mapimpi, 10. Handré Pollard, 9. Faf de Klerk, 1. Ox Nché, 2. Bongi Mbonambi, 3. Trevor Nyakane, 4. Eben Etzebeth, 5. Franco Mostert, 6. Siya Kolisi (capitaine), 7. Pieter-Steph du Toit, 8. Kwagga Smith.
Substitutes: 16. Malcolm Marx, 17. Steven Kitshoff, 18. Frans Malherbe, 19. Lood de Jager, 20. Rynhardt Elstadt, 21. Herschel Jantjies, 22. Elton Jantjies, 23. Damian Willemse.
SPECIAL EVENT: A Virtual Evening with Mike Phillips and Adam Jones on July 29 – Submit your questions here …