The Portuguese was sent off for a high challenge on ex-United striker Andy Cole in the 66th-minute of Saturday's 3-1 defeat at Manchester City.
Although Ronaldo did not make any contact, referee Steve Bennett decided the studs-up challenge was serious foul play and sent him off.
In a statement on its website on Tuesday the English Football Association said its Disciplinary Commission had rejected Ronaldo's claim for wrongful dismissal.
His three-match ban starts immediately, meaning he will miss Wednesday's FA Cup replay against Burton Albion, Sunday's Premier League match at home to Liverpool and the second leg of their League Cup semi-final against Blackburn Rovers on Jan. 25.
