Clarke came to the crease to a chorus of boos from Australian fans dissatisfied with his batting form and unimpressed with his captaincy but left to general applause after top-scoring with 54 in Australia's total of 249.
Chris Woakes took 6-45 to become only the second Englishman after his current teammate Paul Collingwood to claim a six-wicket bag in a one-day international.
Woakes' career-best performance was then undermined by poor top-order batting which saw England dismissed for 198 in 45.3 overs.