No rugby nation gets more out of limited resources than Australia, and those qualities were once more in evidence as they beat England for the eighth time in 12 meetings since the 2003 World Cup final.

Australia arrived fresh from a 30-point hammering in Paris, with coach Robbie Deans pursued by the imprecations of motormouth wing David Campese, and missing some of their biggest names, but none of this was in evidence as they outthought and outmanoeuvred their hosts.

They played almost all the imaginative rugby and held their own in phases, notably the scrum, where England had hoped to establish a clear advantage. Deans said of his team's performance that "it was much better than last week, but it had to be".

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It was a result the significance of which may be felt for a long time. Had England won, they would have vaulted over the Australians to take their place in the top four of the world rankings and with it – should they have retained that place when the draw is made at the end of the month – a top seeding when they host the 2015 World Cup.

Instead, the Wallabies consolidated third place, and all but sealed a top seeding. England are now likely to need victories, a little matter of beating both South Africa and New Zealand, in their remaining autumn matches to make the top four. As England defence coach Andrew Farrell, who has long experience of competing against Australia in both rugby codes, said: "They played a smart game."

It is rare that they do not. The difference was most apparent with the ball in hand. Where England were intent on seeking contact, and looked sluggish in both movement and handling, the Australians offloaded well, ran smart support lines and had a fluency not seen so far this autumn from any of the British and Irish teams.

Their attacking efforts revolved around outside-half Kurtley Beale and full-back Berrick Barnes. Their positions are worth noting, since it is not that long since their positions were reversed, with Barnes in the No 10 shirt and Beale at 15. Both looked completely at ease in their comparatively new roles.

"They managed the game well, and used the variation of the chip over the top very effectively," noted Mike Catt, England's attack coach. That, perhaps, is the key to their success. Having a limited playing pool, they develop all-round footballers rather than specialists. They also made light of the absence of perhaps their most important player, back-row forward David Pocock, the man who vies with Richie McCaw as supreme master of the breakdown.

He was scarcely missed because his deputy Michael Hooper had a magnificent game in breaking up England's attacks with a substantial tackle count and as a vital link in attack.

Neutralised elsewhere, England might still have prevailed had they achieved the scrum dominance attained in some past meetings. It never happened. Australia held their own and England conceded a number of penalties, with the Mohican-coiffured Joe Marler several times attracting referee Monsieur Romain Poite's attention for the wrong reasons.

The vital scoring action was crammed into 18 minutes either side of half-time. England led 9-6 with three penalties from Flood to a drop goal and penalty by Barnes when, after 35 minutes, scrum-half Nick Phipps broke in midfield to send wing Nick Cummins charging to the line. There were hints of obstruction and a forward pass, but these were as nothing compared to the doubts about the England try which followed three minutes later.

Scrum-half Danny Care took a quick tap when England were awarded a kickable penalty. Centre Manu Tuilagi, ignoring Charlie Sharples outside him, stretched for the corner and was awarded the try following a long, and not entirely conclusive, referral to the television match official.

So England led, a little fortuitously, 14-11 at the break, but saw their advantage wiped out within four minutes, and turned into a six-point deficit by the 51st as the variety, pace and width of Australia's attack stretched them into conceding a succession of penalties calmly converted by Barnes.

That was the end of the scoring. England never lacked intent, but could not match it with precision or imagination. They were rightly denied a try when No 8 Thomas Waldrom lost the ball in trying to touch down and, in the final quarter – perhaps influenced by their success in the first half – forwent three potentially kickable penalties to go for tries. These decisions denied them the chance of a draw, but ensured that justice was seen to be done in the final scoreline.

England: A Goode: C Ashton, M Tuilagi, B Barritt, C Sharples: T Flood, D Care: J Marler, T Youngs, D Cole: T Palmer, G Parling: T Johnson, T Waldrom, C Robshaw (captain). Replacements: T Wood for Johnson 50, M Vunipola for Marler 50, J Launchbury for Palmer 54, B Youngs for Care 61, M Brown for Sharples 61, D Paice for T Youngs 73, O Farrell for Barritt 73

Australia: B Barnes: N Cummins, A Ashley-Cooper, B Tapuai, D Loane: K Beale, N Phipps: B Robinson, T Polota Nau, B Alexander: S Timani, N Sharpe (captain): D Dennis, W Palu, M Hooper

Replacements: S Moore for Polota Nau 40, L Gill for Dennis (blood bin 56-67, permanent 76), J Slipper for Robinson 61, D Mitchell for Ioane 70, S Kepu for Alexander 71

Referee: R Poite (France)