The hosts dominated the first half, leaving Australia looking flat-footed, and a solid performance in the second period kept the scoreboard ticking over even after the inevitable Wallabies fight-back kicked in.
But if Flood put in a fantastic performance with the boot, man-of-the-match Ben Youngs easily matched him by dictating play when the ball was in hand; the Leicester scrum-half wreaking havoc all over the park before he picked up a knock and was replaced on 55 minutes by Danny Care.
Out-played, albeit not badly, by New Zealand a week ago England showed no signs of repeating their mistakes as the exploded out of the blocks in a confident manner and refused to let Australia get a grip on the game.
The Wallabies, coming off the back of confidence-boosting wins over the All Blacks and Wales, squandered two chances to take the opening points; James O'Connor seemingly cowed by the crackling atmosphere at Twickenham.
The 20-year-old winger, so solid in scoring the winning try in Hong Kong two weeks ago, suffered a torrid afternoon as he pulled his first two kicks wide of the posts and was repeatedly hammered into the ground with the ball in hand.
O'Connor's England counterpart Flood had no such troubles however, quickly taking advantage of his first chance when Australia were caught offside after a scintillating break by Youngs and Mike Tindall.
England extended their lead in the 24th minute when Tom Croft produced a stylish one-handed offload whilst on the floor to send Ashton crashing over for his first try of the afternoon.
Flood added the conversion before he and O'Connor traded penalties on the half hour mark.
But just as Australia looked as though they might get something going with Beale charging towards the try-line, England turned things around with a clearance kick before swamping a shaky O'Connor at the other end.
Australia desperately tried to clear the ball but Matt Giteau, struggling for form since this summer's Tri-Nations, was sent to the sin-bin for illegally stopping Youngs to recycle the ball.
Flood took the three points on offer, after being denied another try with a quick chip across field to Mark Cueto, and, although Australia responded with another O'Connor penalty on the stroke of half-time, the Wallabies left the field looking stunned.
Things quickly went from bad to worse for the tourists though as Flood added another penalty shortly after the re-start before a moment of brilliance from Ashton almost put the game beyond doubt with 30 minutes still remaining.
Youngs once again was the catalyst as he stole the ball on the Aussie try-line and the Northampton back took full advantage, running the length of the pitch and cutting inside Drew Mitchell for his second try of the match.
Australia flirted with a revival when Kurtley Beale crossed over after following his chip up-field and comfortably out-pacing Ben Foden. And the New South Wales man added another five minutes later after a break down the left by Luke Burgess.
But three more penalties from the boot of Flood meant the Wallabies never came close to causing any concern for Martin Johnson's men as they turned in their best performance for years less than 300 days before the World Cup gets underway in New Zealand.