Fainga'a will start at outside centre following the suspension of James O'Connor, who was banned for one match for sleeping in and missing two official functions.
Adam Ashley-Cooper will move to the wing in the re-shuffle with Quade Cooper taking over kicking duties, while veteran forwards Radike Samo and Dan Vickerman are recalled.
Lock Vickerman will partner new captain James Horwill in the second row while Fijian-born number Samo is named in a starting line-up for the first time since 2004 after an impressive Super Rugby season with the Reds.
"The group showed a lot of character to bounce back in South Africa but no one in our party is getting ahead of themselves," Deans said. "The All Blacks are not the benchmark in world rugby without good reason.
"Obviously there is a lot of rugby coming up in New Zealand, and there will inevitably be expectations around the impact that this weekend might have on that.
"But while a lot is going to happen beyond Saturday, we can't afford to and won't be looking beyond this game."
Australia have not beaten New Zealand in Brisbane since 1992 and lost the previous head-to-head in the Queensland state capital 28-24 in 2008.
Team: Kurtley Beale, Adam Ashley-Cooper, Anthony Fainga'a, Pat McCabe, Digby Ioane, Quade Cooper, Will Genia; Sekope Kepu, Stephen Moore, Ben Alexander, Dan Vickerman, James Horwill, Rocky Elsom, David Pocock, Radike Samo.Repleacements: Saia Fainga'a, Salesi Ma'afu, Rob Simmons, Ben McCalman, Scott Higginbotham, Luke Burgess.
Gilbert has released a new line of rugby cleats. The Gilbert Virtuo 8S is part of the exciting new product. Check it out.
The entire All Blacks apparel line has been updated for 2013/14. Check out the New Zealand All Blacks polo.
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The Gilbert Blitz 8S rugby cleat is a great cleat at a great price of $69.99. Get a new pair of cleats today.
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Wear the crest of the British and Irish Lions on your t-shirt. A great look for the summer.
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The NEW All Blacks 2013/14 jersey has arrived at World Rugby Shop. Dare to wear the colors of the All Blacks.