Mikel had already admitted a charge that he confronted referee Mark Clattenburg in the official's changing room after the game before the personal hearing.
The decision by the Independent Regulatory Commission revealed the sanction, which included a £60,000 fine, would have been "significantly longer" but for the fact Mikel had believed he had been racially abused by Clattenburg.
The suspension will take effect immediately and rule Mikel out of domestic duty until Boxing Day.
"Chelsea's John Obi Mikel has been given a three-match suspension to begin with immediate effect and fined £60,000 following an Independent Regulatory Commission hearing today [Thursday 6 December 2012]," an FA statement read.
"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."
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- Sports & Recreation
- John Obi Mikel
- Mark Clattenburg