Vukovic was initially suspended for nine months for striking the referee in the A-League grand final in February before an independent FFA panel reduced the ban in April, allowing him to play in Beijing in August.
But FIFA on Tuesday reinstated the original punishment, saying to do otherwise would be "contrary to the spirit" of its regulations, FFA said in a statement.
FFA said it would not appeal the decision, although the player can launch a personal appeal if he wants.
He played in all of Australia's 14 Olympic qualifying matches before the suspension.