Thorne replaces Jerry Collins, another ex-skipper, at blindside flanker in the encounter against the Springboks at Jade Stadium, a match they must win to have a chance of retaining the Tri-Nations title.
Mils Muliaina replaces Thorne's Crusaders team-mate Leon MacDonald at full-back, as he did in the 20-15 Bledisloe Cup defeat to Australia in Melbourne last month.
Doug Howlett comes into the starting XV on the right wing with Keith Robinson back at lock, while Conrad Smith starts on the bench.
"Our goal is to improve on the first two Philips Tri Nations Tests," said All Blacks coach Graham Henry.
"We can play better and these two home matches are our last chance to do so before the Rugby World Cup.
"We also want to see some players get more time on the field, so there have been changes to the line up. The challenge is to make sure everyone in the squad is raising the standard."
Ross Filipo and Rico Gear remain with the squad for the Auckland test against Australia replacements for injured duo Ali Williams and Leon MacDonald..
New Zealand team:
Mils Muliaina (Waikato), Doug Howlett, Isaia Toeava (both Auckland), Luke McAlister (North Harbour), Sitiveni Sivivatu; Dan Carter (Canterbury), Piri Weepu (Wellington); Tony Woodcock (North Harbour), Keven Mealamu (Auckland), Carl Hayman (Otago); Chris Jack (Tasman), Keith Robinson (Waikato); Reuben Thorne (Canterbury), Richie McCaw (Canterbury, captain), Rodney So'oialo (Wellington).
Reserves: Andrew Hore (Taranaki), Neemia Tialata, Jerry Collins, Conrad Smith, Chris Masoe (all Wellington), Brendon Leonard (Waikato), Nick Evans (Otago).