The Nigerian international has been suspended for three games and fined £60,000 for 'using threatening and/or abusive and/or insulting words and/or behaviour' in the aftermath of the Blues' loss to Manchester United at Stamford Bridge.
Clattenburg was accused of using racist language toward Mikel but was later cleared and now the player is the one who has been punished by the football association.
"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]," read a statement on the FA's official website.
"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 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."