Flintoff made 42 before falling to a freak return catch by fast bowler Brett Lee.
The England allrounder sweetly struck a drive, but Lee took a superb reflex catch in his follow through.
The last over of England's innings was fittingly bowled by veteran Australia pace bowler Glenn McGrath, in his final game for his country at his home ground.
McGrath (2-41) sent the crowd into raptures when he claimed a wicket with his last ball, Paul Nixon caught by Hodge on the midwicket boundary for six.
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