Rooney was charged with using abusive language while celebrating a goal in Saturday's 4-2 Premier League win at West Ham United.
In a statement on their website the FA said that Rooney had admitted the charge for the use of offensive, insulting and/or abusive language.
"However, Rooney has submitted a claim that the automatic penalty of two games is clearly excessive. A commission will hear the submission on Wednesday," the statement said.
The commission could agree to reduce the ban, impose a fine, or increase the match suspension.
Just before the FA issued their statement, Ferguson, speaking at a news conference at Lord's Cricket Ground ahead of Wednesday's Champions League quarter-final first leg at Chelsea, had said no appeal would be launched.
At present, the England striker will miss United's home league match against Fulham on Saturday and the FA Cup semi-final against Manchester City at Wembley on April 16.
He can play in both legs of the Champions League tie with Chelsea as that competition is not covered by an FA ban.
Ferguson is himself serving a five-match touchline ban imposed for comments he made about the referee following United's league defeat at Chelsea last month.
