Speculation was rife that Cooper would fill the number 12 jersey after the Wallabies lost all three of Matt Giteau, Matt Toomua and Rob Horne to injury last week. but Cheika has opted to put the former Reds fly-half straight into the main playmaking role.
Cooper will combine with usual Wallabies pivot Bernard Foley in a dual playmaker structure, with Foley starting at inside centre for the first time in his Test career.
The move does mean that Cooper and Will Genia will reignite their longstanding partnership in the halves, after playing most of their careers together in Queensland.
The former Red’s inclusion is far from the only change in a Wallabies team shake-up, with Cheika ringing the changes after last weekend's 42-8 loss in Sydney.
Rob Simmons has been dropped from the side entirely after New Zealand’s domination of the Australian lineout last week, and didn't travel with the team to New Zealand.
Simmons has been replaced by Adam Coleman in the second row, with the Force lock pairing up with Kane Douglas adding more fire to that area of the game.
Blindside flanker Scott Fardy has regained his starting spot, playing alongside Michael Hooper and David Pocock in the Wallabies back row.
Samu Kerevi has also impressed Wallabies coach MIchael Cheika enough to start at outside centre for the second match up, a direct swap for Tevita Kuridrani, who has struggled for form in recent Tests.
That decision is a major tick of approval for Kerevi, with Kuridrani one of the mainstays of Cheika's Wallabies tenure.
Kuridrani has been named on the bench, alongside rookie utility back Reece Hodge and scrum-half Nick Phipps as backs replacements, while Dean Mumm and Will Skelton will be injected off the bench for the forwards.
As well as Simmons, none of Drew Mitchell, Luke Morahan or Ben McCalman travelled with the team to Wellington on Wednesday night, while Nick Frisby was a surprise addition to the touring squad.
15 Ben Smith, 14 Israel Dagg, 13
Malakai Fekitoa, 12 Anton Lienert-Brown, 11 Julian Savea, 10 Beauden
Barrett, 9 Aaron Smith, 8 Kieran Read (c), 7 Sam Cane, 6 Jerome Kaino, 5
Samuel Whitelock, 4 Brodie Retallick, 3 Owen Franks, 2 Dane Coles, 1
Substitutes: 16 James Parsons, 17 Wyatt Crockett, 18 Charlie Faumuina, 19 Liam Squire, 20 Ardie Savea, 21 TJ Perenara, 22 Aaron Cruden, 23 Seta Tamanival
15 Israel Folau, 14 Adam Ashley-Cooper, 13 Samu Kerevi, 12 Bernard Foley, 11 Dane Haylett-Petty, 10 Quade Cooper, 9 Will Genia, 8 David Pocock, 7 Michael Hooper, 6 Scott Fardy, 5 Adam Coleman, 4 Kane Douglas, 3 Sekope Kepu, 2 Stephen Moore, 1 Scott Sio
Substitutes: 16 Tatafu Polota-Nau, 17 James Slipper, 18 Allan Ala’alatoa, 19 Dean Mumm, 20 Will Skelton, 21 Tevita Kuridrani, 22 Reece Hodge, 23 Nick Phipps