Substitute Scott Staniforth claimed the crucial try with just eight minutes remaining as the Wallabies secured their first win over the All Blacks since 2004.
Wallabies captain Stirling Mortlock produced a man-of-the-match performance, having a hand in both second-half tries - the other scored by Adam Ashley-Cooper - and starting many of the Wallabies' forward forays.
Richie McCaw led the All Blacks from the front, but the yellow card received by Carl Hayman in the 61st minute proved to be a major turning point.
Mils Muliaina made an early break from an inside pass and Tony Woodcock dived over for his first Test try and the opening five-pointer after four minutes. Dan Carter landed the conversion from the sidelines.
Mortlock missed a penalty goal from 40 metres out after 10 minutes but made up for his inaccuracy by landing a simple kick from straight in front to bring the score back to 7-3.
Carter pushed the margin back out to a converted try with a simple penalty goal after George Smith was penalised for offside, before Mortlock once again reduced the margin to four with a pinpoint kick from a slight angle.
In the 25th minute, the All Blacks spread the ball wide as Luke McAlister beat two defenders with ease and found Rico Gear to touch down out wide.
With the All Blacks holding a comfortable lead at half-time, the Wallabies attacked as the second period began.
Mortlock found a gap in the All Blacks' defence but was brought down inside the Wallabies 22, before Guy Shepherdson fell agonisingly short of the line.
The All Blacks were reduced to 14 men when Hayman was given his marching orders for an infringement at the breakdown and the Wallabies seized the advantage as Ashley-Cooper scored an excellent solo try.
After some excellent play from Mortlock, Nathan Sharpe found Ashley-Cooper with a superb pass before the winger beat Gear and held off McCaw and Chris Jack to score in the corner.
Giteau nailed the conversion to reduce the margin to two points as the Wallabies continued to attack.
Carter missed an easy penalty goal from a slight angle and Staniforth made the All Blacks fly-half pay for his mistake by crossing for the Wallabies' second try late on.
Mauger kicked out on the full before Mortlock made a tremendous run down the middle of the ruck, finding Staniforth with an overhead pass for a try under the uprights. Giteau converted easily.
The Kiwis tried hard in the final minutes to find a late winner, but the Wallabies held out.