New skipper James Horwill led the Wallabies a week-and-half after taking over the captaincy from Rocky Elsom and his side raced into a 20-3 lead by the interval.
Will Genia darted over from close-range early on before No8 Radike Samo, making his first Test start in seven seasons, powered home from fully 60 metrres.
But just as they had done in successive games against the Wallabies last year, the All Blacks hit back to level the scores thanks to tries from centre partners Conrad Smith and Ma'a Nonu.
The Wallabies were not to be denied a famous triumph, however, with full back Kurtley Beale scoring the decisive try after Genia instigated an impressive team move.
As well securing just their third southern hemisphere crown in 16 years of competition, a second win over the All Blacks in 12 attempts and a first in Brisbane for 19 years proved the perfect way to finish their preparations for next month's World Cup.
Those preparations started appallingly with a shock defeat to Samoa in July but home and away wins over World Champions South Africa and this final day success over their greatest rivals sees the Wallabies head across the Tasman Sea in high spirits.
Victory also gives the Lions an early indication of the size of the challenge they will face when they head to Australia in two years time.
With young stars such as Genia, Quade Cooper, Beale and today's absent wing James O'Connor fast becoming the backbone of the Australian side, Britain and Ireland's elite look set to have their hands full when they attempt to gain revenge for their series defeat 10 years ago.