England (14) 14
Pens: Flood 3
Australia (11) 20
Pens: Barnes 4
Drop goals: Barnes
Australia regained the Cook Cup with as Berrick Barnes' four penalties helped edge an uncertain England at Twickenham.
After two successful Barnes penalties in the first half kept the visitors in touch, after Manu Tuilagi's try handed England an interval lead, the full back struck three times early in the second period to kill off the home side.
England wasted a series of opportunities to regain parity in the second 40 minutes, but opted to run the ball instead of kicking for goal as Robbie Deans' side hung on and bounced back from their crushing defeat in Paris a week ago.
The result cements Australia's place in the top four of the IRB world rankings, while England will now require wins against South Africa and New Zealand in the following fortnight should they wish to be among the seeded teams for the World Cup in 2015 on home turf.
Stuart Lancaster welcomed back Chris Ashton fro the start following last weekend's suspension in place of Ugo Monye, as Charlie Sharples regained his place having scored two trys against Fiji.
Despite the emphatic start to their autumn series against the Pacific Islanders, England dropped out of the top four in the IRB world rankings after France claimed an unlikely 33-6 win over Australia in Paris last weekend to leap-frog their Six Nations rivals.
However, victory against a much criticised and wounded Wallabies side would reinstate England in that top four, with two QBE internationals against South Africa and New Zealand to follow.
Australia made four changes from the humiliation in the French capital, with injured trio David Pocock, Kane Douglas and Pat McCabe, along with the suspended Rod Simmons making way for Sitaleki Timani, and Ben Alexander in the pack and Ben Tapuai and Digby Ioane in a reshuffled midfield, with Adam Ashley-Cooper installed at No.13.
After Flood had handed England an early lead with a second minute penalty, it was Australia who enjoyed the early possession, with Ben Tapuai and Ashley-Cooper both attempting to force their way, and as the hosts' defence continued to frustrate, Barnes' drop goal ensured the away side drew level.
Flood and Barnes then exchanged penalties but upon the England fly half kicking his third penalty of the afternoon, the Wallabies sprung into action as Nick Phipps evaded two tackles and fed Cummins who finished in the corner.
But Australia's lead lasted just two minutes as Tuilgai, despite the attention of Kurtley Beale and Phipps, was adjudged to have grounded the ball on the try line to hand England, if not the momentum, but the advantage at the interval.
England were unable to stem the flow of possession or indiscipline and they went six points behind inside 13 minutes of the second half as Barnes kicked three penalties in succession.
The six-point deficit sparked England into life and Ashton came within meters of the line before a succession of catch and drives from five-metre line-outs saw Thomas Waldrom fail to ground the ball.
An insistence on kicking away possession had been eliminated from the first half, as the introduction of Mako Vunipola ensured quicker ball for the England backs, and in stark contrast to the first half, it was the Australian defence which was put under constant pressure.
Despite England being camped in the opposition half they couldn't force a decisive score, as Lancaster's side continued to run the ball rather than take the points on offer via penalties as first an Australian boot disrupting replacement Ben Youngs and then Mike Brown knocking on 10 meters out.
And as Tuilagi's knock-on in England's final attack of the match produced yet another error during a frustrating afternoon it was left to Australia to run down the clock and record a 24th Cook Cup victory.
England: A Goode, C Ashton, M Tuilagi, B Barritt, C Sharples, T Flood, D Care; J Marler, T Youngs, D Cole, G Parling, T Palmer, T Johnson, C Robshaw (capt), T Waldron.
Replacements: D Paice (for T Youngs 64), D Wilson, M Vunipola (for J Marler 50), J Launchbury (T Palmer 53), T Wood (for T Johnson 50), B Youngs (for D Care 61), O Farrell 64). M Brown (for C Sharples 61).
Australia: B Barnes, D Ioane, A Ashley-Cooper, B Tapuai, N Cummins, K Beale, N Phipps; B Robinson, T Polota Nau, B Alexander, S Timani, N Sharpe (capt), D Dennis, M Hooper, W Palu.
Replacements: S Moore, (for T Polata Natu) J Slipper, S Kepu (for B Alexander 70), R Samo, L Gill (for D Dennis), B Sheehan (for D Dennis 58), M Harris, D Mitchell (for D Ioane 68).