There is also a welcome return to the reserves for 36-test forward Scott Barrett, after a four-month injury layoff.
In the backs, Anton Lienert-Brown has been named at centre, while Rieko Ioane will provide impact from the bench.
George Bridge, who suffered a serious pectoral injury in training on Wednesday, makes way for Clarke on the left wing.
Beauden Barrett resumes his position at fullback after his late withdrawal last week, with Damian McKenzie on the bench.
All Blacks head coach Ian Foster was happy with the team's preparation ahead of the grudge match at Eden Park.
"Our preparation this week has been really good," he said.
"It was our first test together last weekend and while there were some aspects of our game that we were pretty excited about, especially around our set piece, we didn't get the performance that we wanted, so there has been plenty for us to work on. We need to be smarter with our ball and more focussed defensively.
"The Bledisloe series is back to square one and starts again this weekend, which is exciting. It's the last test at home for us so there will also be massive excitement amongst our fans. There is everything to play for and we can't wait."
On the selection of Vaa'i and Hodgman, Foster added: "It's a great opportunity for Tupou. We enjoyed seeing him come off the bench last weekend, he brought a lot of energy and he has settled in well.
"Alex has been impressive in the training weeks. He's mobile and he's been making big strides in his scrummaging, so it's a big opportunity for him in his first test."
The All Blacks and Australia will be playing their 168th test against each other. New Zealand has won 115 of those matches, Australia 44 with eight draws. The All Blacks have held the Bledisloe Cup since 2003.
All Blacks team:
1. Joe Moody (47)
2. Dane Coles (70)
3. Ofa Tuungafasi (36)
4. Patrick Tuipulotu (31)
5. Tupou Vaa'i (1)
6. Shannon Frizell (10)
7. Sam Cane (69) - captain
8. Ardie Savea (45)
9. Aaron Smith (93)
10. Richie Mo'unga (18)
11. Caleb Clarke (1)
12. Jack Goodhue (14)
13. Anton Lienert-Brown (44)
14. Jordie Barrett (18)
15. Beauden Barrett (84)
Reserves:
16. Codie Taylor (51)
17. Alex Hodgman - debut
18. Nepo Laulala (27)
19. Scott Barrett (36)
20. Hoskins Sotutu (1)
21. TJ Perenara (65)
22. Rieko Ioane (30)
23. Damian McKenzie (24)