His place will be taken by Highlanders centre Seilala Mapusua with Umaga's Hurricanes team-mate Tane Tu'ipulotu moving on to the Probables bench.
"We want Tana healthy, that's the most important thing," said All Blacks coach Graham Henry. "Resting him is the sensible thing to do."
A new Probables captain will be named closer to the match.
There are also changes to the Possibles line-up with lock Ross Kennedy forced to withdraw because of a knee injury.
The Hurricanes second row has played through much of the Super 12 with a meniscal tear and has opted for surgery but is hopeful of playing for Wellington against the British & Irish Lions on June 15.
Highlanders' Tom Donnelly now starts in the number four jersey with Bryce Williams, who missed the Super 12 after having a shoulder reconstruction, on the bench.
"We also understand and support Ross Kennedy's decision to have surgery sooner rather than later," said Henry.
"If he has the operation now, there's a good chance he will be available for Wellington's match against the Lions."
The New Zealand Maori team have first call on players for their clash with the Lions and the first-choice players from the Crusaders side omitted after their victory over the New South Wales Waratahs in the Super 12 final last weekend.
The Probables and Possibles teams are missing players like Daniel Carter, Chris Jack, Richie McCaw, Justin Marshall, Aaron Mauger, Greg Feek, Carl Hayman, Jono Gibbes and Marty Holah, who will be involved when the All Blacks take on the Lions in three Tests during June and July.
Probables: Sosene Anesi; Doug Howlett, Mils Muliaina, Seilala Mapusua, Sitiveni Sivivatu; Nick Evans, Byron Kelleher; Tony Woodcock, Derren Witcombe, Campbell Johnstone, James Ryan, Ali Williams, Sione Lauaki, Craig Newby, Steven Bates.
Reserves: Keven Mealamu, Clarke Dermody, Bradley Mika, Rodney So'oialo, Jimmy Cowan, Andrew Mehrtens, Tane Tu'ipulotu.
Possibles: Ben Atiga; Scott Hamilton, Conrad Smith, Ma'a Nonu, Brent Ward; Stephen Donald, Steve Devine; Saimone Taumoepeau, Andrew Hore (captain), John Afoa, Tom Donnelly, Kevin O'Neill, Chris Masoe, Josh Blackie, Nick Williams.
Reserves: Tone Kopelani, Carl Hoeft, Bryce Williams, Jerry Collins, Jamie Nutbrown, Jimmy Gopperth, Casey Laulala.