Mils Muliaina began at centre ahead of Conrad Smith and Isaia Toeava, Luke McAlister was picked rather than Aaron Mauger at second five-eighths and Keith Robinson came off little match-play to lock the scrum rather than Chris Jack.
The All Blacks led 13-3 at the break and looked comfortable despite some glitches. McAlister was sin-binned, Carter left without making much impact and his replacement Nick Evans was injured.
France drew level, then Rodney So'oialo scored, but a countering French attack, including a forward transfer to Yannick Jauzion and conversion, gave France a shock lead they would not surrender.
"Obviously we are disappointed but that's sport, I guess," coach Graham Henry said. "We didn't play as well as we have done in the past and the French played particularly well in defence. I thought they were very astute in their game plan and they took their opportunities."
Everything, Henry said, was done to have the All Blacks peak for the playoffs. New Zealand Rugby agreed to those requests and the side departed from the World Cup at an earlier stage than ever before.
Subsequently, a stunned Henry urged an IRB investigation into the performance of referee Wayne Barnes and contemplated match-fixing as the only logical explanation.
His analysis suggested France deserved to be penalised 40 times in the match, while the All Blacks received just two penalties.