The referee was cleared of any misbehaviour, and Mikel's ban will start with Saturday's match against Sunderland.
The statement on the FA's official website read: "Chelsea's John Obi Mikel has been given a three-match suspension to begin with immediate effect and fined 60,000 pounds following an Independent Regulatory Commission hearing today (Thursday 6 December 2012).
"Mikel had requested a personal hearing after admitting an FA charge of using threatening and/or abusive and/or insulting words and/or behaviour.
"The breach of FA Rule E3 was in relation to an incident which occurred in the match official's changing room at the end of Chelsea's fixture against Manchester United on 28 October 2012.
"The Regulatory Commission’s independent chairman Christopher Quinlan QC emphasised that the Independent Regulatory Commission accepted, as did The FA, that at the time he threatened the referee the player genuinely believed that the referee had racially abused him.
"But for that factor the suspension would have been significantly longer.
"Subsequently the FA investigated the allegation that the referee racially abused the player and found that there was not a case for him to answer."