The 22-year-old must forfeit 15% of his match fee from the Perth ODI for breaching the ICC's code of conduct.
Stokes was charged with "using language or a gesture that is obscene, offensive or insulting" for his reaction to claiming the wicket of James Faulkner.
"Mr Stokes's reaction was a clear breach of the code, as players are expected to respect their opponents at all times, no matter what the match situation is. This is a cornerstone of how we play the game," said match referee Andy Pycroft.
Stokes had argued that his reaction to getting Faulkner out was 'nothing worse than what he had been getting from Australia's bowlers all series'.