Carter, who won the second test for the All Blacks in Christchurch with a dramatic last-minute drop goal, has a hamstring injury which All Blacks management said he suffered during training in Hamilton on Tuesday.
Head coach Steve Hansen said: "He has suffered a mild hamstring strain to his right leg which has unfortunately ruled him out of this weekend's test. He will undergo further assessment over the next few days to determine when he will be fit to return to rugby."
Cruden's inclusion is one of six changes to the team which won 22-19 in the thrilling encounter at AMI Stadium.
Kieran Read has predictably been ruled out with injury - his head knock in Christchurch was the second in two weeks - with skipper Richie McCaw moving to No8 and Sam Cane at openside flanker in his first test start.
Chiefs loose forward Liam Messam, brought into the squad as cover on Sunday, starts at blindside flanker, in place of Adam Thomson, who drops to the reserves.
There are two other changes in the backs, with last week's wings Zac Guildford and Julian Savea replaced by Hosea Gear and Ben Smith.
New cap Beauden Barrett comes into the reserves, with Tamati Ellison on the bench as outside back cover.
In the forwards, 26-year-old Luke Romano will make his test debut in the second row alongside fellow Crusader Sam Whitelock, replacing Brodie Retallick who is on the bench.
Hooker Keven Mealamu returns from his calf injury and is on the bench. That's one positive for the All Blacks but the loss of Carter and Read are massive ones for a team hoping to maintain its unbeaten record against Ireland.
Chiefs player Cruden, a 23-year-old with only 10 caps, will quickly have to get up to speed in what will be a high-pressure environment, while Read has been in outstanding form and his ball carrying and work at kick re-starts in particular will be hard for McCaw to replicate.
The Irish will be encouraged by their defence and second-half scrum dominance and will be hoping for bad weather in Hamilton on Saturday. They showed in the freezing conditions in Christchurch that they much prefer a physical battle to a free-flowing one.
In naming the side, Hansen said of last weekend's test: "It was a tough, high-pressure test. It said a lot about the character of both teams and I believe this third test will see the same character and composure needed.
"The All Blacks, by their own admission, weren't happy with the way they performed on Saturday, and in part this is a credit to the way the Irish played. They have laid down a challenge and the key will be now how we respond."
This Saturday will be McCaw's 100th test match start. Just two other forwards have more test match starts - South Africa's Victor Matfield (105) and England's Jason Leonard 104.
Ireland have been based in Queenstown for the week and travel to Hamilton this afternoon after naming their team.
All Blacks team to play Ireland at Waikato Stadium in Hamilton on Saturday, kick-off 7.35pm, is: Israel Dagg, Ben Smith, Conrad Smith, Sonny Bill Williams, Hosea Gear, Aaron Cruden, Aaron Smith, Richie McCaw (c), Sam Cane, Liam Messam, Sam Whitelock, Luke Romano, Owen Franks, Andrew Hore, Tony Woodcock. Reserves: Keven Mealamu, Ben Franks, Adam Thomson, Brodie Retallick, Piri Weepu, Beauden Barrett, Tamati Ellison.
