Carter broke his leg playing for the Canterbury Crusaders in the Super Rugby final and missed the entire Rugby Championship after suffering repeated setbacks in his recovery.
All Blacks coach Steve Hansen had hoped to have the world class pivot back in his side for the match against in Brisbane but Carter strained his leg in a recent provincial match.
"We won't take him to Brisbane, and DC believes this as well, that we are better to get him going and confident and happy in himself in his game," Hansen told New Zealand's Radio Sport.
"If all goes well, then we will take him on the end of year tour and he is likely to start against USA," he added of the one-off match in Chicago next month.
New Zealand are already assured of retaining the Bledisloe Cup after a 12-12 draw and 51-20 victory in their first two matches against Australia this year.
Carter's absence is likely to mean a recall for Aaron Cruden, who was dumped for the final two matches of the Rugby Championship after missing a flight to Argentina the morning after a boozy night out.
Cruden is expected to compete for the starting fly-half position with Beauden Barrett, who wore the number 10 shirt in the Rugby Championship-winning match in Argentina and the loss to South Africa in Johannesburg last weekend.
Hansen also confirmed that utility back Ben Smith would miss the match in Chicago after already being ruled out for Brisbane.
"He lost 6kg in that last week and is showing signs of wear and tear," Hansen said of Smith's fatigue on tour. "He will come back in against England."
After playing the United States, the All Blacks travel to Europe to take on England, Scotland and Wales.