Steven Smith scored 70 and Mitch Marsh smashed 64 off 31 balls to help Australia reach 309-7 at Lord's. England was all out for 245 in 42.3 overs with captain Eoin Morgan top-scoring on 85.Australia leads the five-match series 2-0.
Stokes was out for 10 to the extremely rare dismissal of "obstructing the field." He drove a delivery back to bowler Mitchell Starc, who collected the ball and tried to run out Stokes. Taking evasive action, Stokes used his hand to stop the ball and was given out in a decision which upset Morgan.
"It's difficult. A guy throws the ball in your direction and all you can do is flinch. You don't have time to think," Morgan said. "It was a natural reaction to avoid the ball. Mitchell Starc was about five yards away from Ben Stokes."
Smith said: "I probably don't know the laws right to the tee but if you wilfully put your arm out you're given out and that's the way it went."
Stokes is only the seventh batsman in international cricket to be dismissed for obstructing the field.
In a match full of incidents, Australia opener David Warner will miss the rest of the ODI series with a broken left thumb. He retired hurt after being struck by a rising delivery from Steven Finn off only the second ball of the day.
Smith and George Bailey (54) put on 99 for Australia's second wicket, before the middle order contributed through Glenn Maxwell (49) and Shane Watson (39).
Marsh cut loose, hitting seven fours and three sixes before getting dismissed off the final ball of the innings. Stokes finished with 3-60.
A wet outfield delayed the start by an hour, reducing the match to 49 overs per side.
Morgan was the last man out for England after sharing a 51-run third wicket partnership with James Taylor (43) and 55 for the ninth wicket with Liam Plunkett (24). Pat Cummins took 4-56.
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