Thomson is available after serving a one-week one ban imposed after he was cited for stamping on Scotland forward Alasdair Strokosch's head at Murrayfield 11 days ago.
But the International Rugby Board has now appealed what it describes as the leniency of that sanction, and the All Blacks coaches did not consider him for this weekend's clash.
Thomson was not involved in last Saturday's encounter against Italy in Rome. He was yellow-carded for the Strokosch incident, and subsequently cited, which meant him appearing before independent judicial officer Jean Noel Couraud.
He decided on an initial two-week suspension, but that was then cut in half due to Thomson's good conduct at the hearing.
The IRB said on Wednesday night, though, that they would appeal the Thomson outcome.
All Blacks head coach Steve Hansen has still selected a side containing 745 caps that includes star players Dan Carter and Richie McCaw returning as the world champions seek a 25th successive victory over Wales, stretching back 59 years.
Wales, in contrast, will go into the game on the back of successive home defeats against Argentina and Samoa.
Thomson apart, hooker Keven Mealamu was not considered because of a calf muscle injury, while Tamati Ellison (toe) and Beauden Barrett (ribs) are also out.
Hansen, a former Wales coach, said: "We have always known this game will be a fiercely-contested match.
"The Welsh team in the last 12 months have been Grand Slam winners and 2011 Rugby World Cup semi-finalists.
"We have known since the World Cup that this would be the game that they would be targeting in this autumn series, so any recent performances or results won't have any bearing on this match.
"We are all excited by what comes with this challenge, along with the fact that we will be playing in one of the world's greatest rugby stadiums."
While New Zealand are targeting a 20th successive Test match unbeaten, Wales are facing a sixth defeat on the bounce.
If that happens, it would be their worst run of results since 2002-03 - when Hansen was in charge - when they lost 10 games in a row.
New Zealand team to play Wales at the Millennium Stadium on Saturday: I Dagg; C Jane, C Smith, M Nonu, J Savea; D Carter, A Smith; T Woodcock, A Hore, O Franks, L Romano, S Whitelock, L Messam, R McCaw (capt), K Read.
Replacements: D Coles, W Crockett, C Faumuina, B Retallick, V Vito, P Weepu, A Cruden, B Smith.
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