Australia survived a spirited England fightback to hand new coach Andy Robinson his first defeat as they won 21-19 at Twickenham for the first time since 1998.
England ultimately paid the penalty for a below-par first-half display after their victories over Canada and South Africa in the opening two autumn internationals.
Australia's outstanding centre Matt Giteau, who had set up their first-half tries for hooker Jeremy Paul and full-back Chris Latham as well as kicking a 42nd-minute penalty, had the final say with two more late penalties.
Australia's other points came from fly-half Elton Flatley who converted Paul's opening try before retiring hurt midway through the first-half.
After England were totally out-played in the first-half their forwards were transformed after the interval as they turned on the power.
Lewis Moody opened their account after the pack drove him over for a 48th minute try with wingers Josh Lewsey and Mark Cueto both crossing in the space of three minutes midway through the second half.
Centre Mike Tindall, England's third kicker of the afternoon converted both to edge his side 19-15 ahead but Australia proved they can never be written off with Giteau's two late penalties.
In the end England showed just how badly they are missing the injured Jonny Wilkinson.
Fly-half Charlie Hodgson, outstanding in last week's win over South Africa, squandered two simple first-half penalties and then scrum half Andy Gomarsall missed an even simpler conversion.