McAlister, who impressed in the New Zealand Maori team's 35-28 win over England in midweek, was brought in as a precaution should Carter's thigh strain flare up.
All Blacks management said on Thursday Aaron Cruden would start in the number 10 jersey should Carter, who scored 27 points in a 42-9 mauling of Wales last weekend, be unavailable.
Wales, meanwhile, have dropped their own fly-half Stephen Jones to the bench for Hamilton test because of a thumb injury suffered in the first game.
Twenty-year-old Dan Biggar will replace him while Jonathan Davies has been brought in at centre for Andrew Bishop, who hurt his hand in the first test at Carisbrook.
New Zealand named their 22 on Tuesday.
Wales: Lee Byrne, Leigh Halfpenny, Jonathan Davies, Jamie Roberts, Tom Prydie, Dan Biggar, Mike Phillips, Ryan Jones (captain), Gavin Thomas, Jonathan Thomas, Alun Wyn Jones, Bradley Davies, Adam Jones, Matthew Rees, Paul James.
Replacements: Huw Bennett, Craig Mitchell, Deiniol Jones, Rob McCusker, Richard Rees, Stephen Jones, Will Harries.
New Zealand: Mils Muliaina, Cory Jane, Richard Kahui, Benson Stanley, Zac Guildford, Daniel Carter, Jimmy Cowan, Kieran Read, Richie McCaw (captain), Jerome Kaino, Tom Donnelly, Brad Thorn, Neemia Tialata, Keven Mealamu, Tony Woodcock.
Replacements: Aled de Malmanche, Owen Franks, Tom Sam Whitelock, Adam Thomson, Piri Weepu, Aaron Cruden, Rene Ranger