Half-centuries from opener Shane Watson and George Bailey helped Australia to a mediocre total of 251 for seven from their 50 overs as England’s bowlers contained the tourists very effectively.
Ian Bell led from the front for England with 75, before Ravi Bopara took control with a brisk 82 before being run-out two balls before Eoin Morgan (43) struck the winning runs with more than four overs to spare.
England’s victory, their first in the format at The Oval since 1997, ensures Alastair Cook’s side claim a second successive win in the series.
If the hosts were to secure a series whitewash, Andy Flower’s men would usurp their tourists at the top of the ICC world rankings and become the first side to be top in all three formats.
Opener Watson's half-century had hinted at much better in Australia’s innings after Clarke won the toss, only for the tourists to falter alarmingly in the middle overs.
Watson moved past his half-century with an eighth four at a run-a-ball, but stalled thereafter while George Bailey’s career-best score was tortuous for long periods as the runs dried up.
The tourists reached three figures in the 20th over. But there was just one boundary, for the loss of Clarke's wicket, in the next 10 overs as England’s bowlers restricted their opponents.
Jade Dernbach took the new ball alongside Steven Finn, as the latter saw off the dangerous David Warner early. Watson had some fortune on his side, dropped by Jonathan Trott in the gully on eight off Dernbach and twice surviving via DRS when Stuart Broad thought he might have him lbw.
There was a half-hour rain stoppage midway through the 12th over, and Broad interrupted any momentum when he had Forrest deflecting the ball down the leg-side with Craig Kieswetter taking a stunning snaffle.
Bopara's part-time medium-pace immediately brought the substantial bonus of Clarke's wicket, caught behind off an inside-edge.
Bailey and David Hussey, who was brilliantly run out by Finn, did enough in a stand of 78 to just about keep Australia in the game before Bresnan dismissed Bailey for the first of two wickets in four balls as Matthew Wade followed.
England's reply did not need to be much more than steady, all the more so after a wayward first two overs with the new ball from the enigmatic and much-derided Mitchell Johnson.
Cook was trapped lbw for 18 by first change Clint McKay, and Trott was bowled off an inside-edge for 17 as he advanced to Watson.
But Bell consolidated superbly as he continued his prolific form since replacing the retired Kevin Pietersen. Matthew Wade dropped him on 38, standing up to Watson, but after David Warner did likewise at point at the start of Brett Lee's second spell, Bell kicked on.
The Warwickshire man was eventually bowled by Clarke, who brought himself on after exhausting all his other options, as he attempted a rash cut to a straight ball which was fuller than he had anticipated.
Morgan was saved by DRS, and the faintest of inside edges according to Hostpot, when Clarke - and umpire Richard Illingworth, initially - thought he was gone lbw for a second-ball duck. That moment of controversy passed, and England’s progress was serene.
The only further set-back for England was Bopara’s dismissal after he managed to run himself out two runs short of the finish line.
England clinched a comprehensive victory with 26 balls remaining, and Australia coach Mickey Arthur was left to bemoan an insipid display from his side in what was a match he had previously described as “must win”.
The third one-day international is a day-night match at Edgbaston on Wednesday.