After warming up in drizzly conditions, both sides returned to the field shortly before kick-off only to be greeted by torrential rain.
Better suited to the slippery conditions, the All Blacks took an early lead thanks to some accurate kicking by playmaker Dan Carter.
But in a competitive opening 40 minutes, the Wallabies made equally good use of their chances to trail just 12-9 at half-time.
After the break, penalty goals continued to be the only source of points for both sides until two personnel changes by New Zealand boss Graham Henry gave his side the impetus in attack.
With reserve scrum-half Brendon Leonard and hooker Keven Mealamu sent into the fray, the All Blacks scored the match's only try in the 58th minute when prop Tony Woodcock crossed the line from close range, before another Carter penalty in the dying stages sealed the result.