Koppe has not been in the best form of late and the return of skipper Faf du Plessis will see Duminy sitting on the sidelines for the next five days.
Of the axing, Du Plessis says: "He will be the first guy to acknowledge that runs are what guarantee you to play in the team, your performances.
“His performances haven’t been consistent enough so we will be giving someone else an opportunity.”
After losing the first Test by 211 runs and then also having fast bowler Kagiso Rabada banned, while coach Russell Domingo is back in South Africa following the death of his mother, Du Plessis knows his team is up against the odds.
He adds: “That stuff that’s been going wrong off the field, is not stuff you can plan for.
“I didn’t expect [my] baby to come a little earlier, Russell’s not planned for the tragedy with his family, and then KG... this is just a huge character test for us.”
Faf, who celebrated his 33rd birthday yesterday, says: “It feels like a normal game for me. I just feel there was more required from me this week to step up and make sure I lead the team the way I’ve been doing.”