It will be the All Blacks' 450th Test and Cowan is restored to the side after playing so well in the opening win over Australia in Auckland. He replaces Brendon Leonard having acted as the water boy in Bloemfontein.
"I was obviously very disappointed to be dropped for the Bloemfontein game. I had to make a sacrifice for the team and get the other 22 players up for the game," said the 27-year-old Cowan.
"It's a hard pill to swallow, but we are in the professional game now and these things happen."
The other change to the side is in the front row where Owen Franks takes over from the injured Neemia Tialata. Franks' place among the replacements goes to John Afoa.
Cowan's task will be to set the back line moving after the worst try return in 15 years for the All Blacks - a mere eight tries in five outings this year. The average in the professional era at this stage of the season is 26.
"We were trying to play a lot of rugby in our own half and while we tried to do that we made a lot of mistakes along the way. I think that was half our problem and the defending takes a lot of energy out of the boys," said Cowan.
"Our big issue was that we didn't play field position and territory, we played in our own half. Something we have looked at as a team is how to get down into their half."
New Zealand's head coach, Graham Henry, felt his side could have won in Bloemfontein after hitting back to 20-16, but admitted it would have been a smash and grab raid had they overhauled John Smit's men.
The need for greater accuracy and less mistakes is obvious, but if there is one team in the world that can hit back from a defeat it is the All Blacks. With 334 wins and 17 draws in their 449 Tests to date, they have an incredible 75% success rate at international level.
"We felt there were weaknesses we could exploit that will enable us to break down their defence better," said Henry,
"But, of course, in rugby you always have to factor in that the opposition will know about those weaknesses and will be working on them this week. It's all about thinking on the hoof in this game.
"I thought we were building towards something in the second half in Bloemfontein, I thought we made a big improvement, and at the stage of the game when we were 20-16 behind I thought we might still escape with a win.
"I am not saying we would have deserved to win, but we were right in it, and with the elimination of errors and basic mistakes that we made in that match there is no reason why we cannot change the result this time.
"I said that last week's Test in Bloemfontein would be a massive challenge and this weekend's Test in Durban is no different. But this team has a lot of character and resolve and we are approaching it in a positive frame of mind."
New Zealand (v South Africa, Durban)
15. Mils Muliaina.
14. Joe Rokocoko
13. Conrad Smith
12. Ma'a Nonu
11. Sitiveni Sivivatu
10. Stephen Donald
9. Jimmy Cowan
1. Tony Woodcock
2. Andrew Hore
3. Owen Franks
4. Brad Thorn
5. Isaac Ross
6. Jerome Kaino
7. Richie McCaw (captain)
8. Rodney So'oialo
16. Keven Mealamu
17. John Afoa
18. Jason Eaton
19. Kieran Read
20. Piri Weepu
21. Luke McAlister
22. Cory Jane