A statement from the Football Association read: "The FA has concluded its investigation into alleged misconduct by Mark Clattenburg during the match between Chelsea FC and Manchester United FC on 28 October.
"No disciplinary action will follow against Mr Clattenburg."
Chelsea had accused the referee of using inappropriate language towards midfielder Mikel in their 3-2 home defeat by their Premier League rivals.
But the FA decided there was "no case to answer" over the allegation the referee said "shut up you monkey" to the Nigerian midfielder. While Mikel did not hear the alleged comment, team-mate Ramires claimed he heard such words.
It will be a huge relief for the 37-year-old official from County Durham who vehemently denied the accusations.
Clattenburg said the prospect of losing his job despite being innocent had been "truly frightening". He will now be available to work having opted not to officiate while the FA conducted its investigation.
"I am looking forward to putting this behind me and concentrating on refereeing in the Premier League and other competitions," Clattenburg added.
He said the last few weeks had been "the most stressful of his life".
Referees chief Mike Riley added: "We are all relieved that this is now behind him and that he can return to doing something that he loves.
"To reduce the risk of an episode of this nature being repeated PGMOL will introduce recording of the referees' communication system on a private basis."
The FA stated the evidence had been considered by independent QC David Waters who ruled Ramires' claim was not supported by any other evidence and disputed by the other match officials.
The FA statement added: "Moreover it was contradicted by other witnesses and does not cross the evidential threshold required to bring a charge against Mark Clattenburg.
"Having considered Counsel's opinion, and in view of all the circumstances of the case, The FA does not believe that there is a case for Mr Clattenburg to answer.
"The FA is satisfied that the allegation against Mark Clattenburg by Ramires was made in good faith. It is entirely possible for a witness to be genuinely mistaken and convincing in his belief.
"The FA receives and investigates numerous allegations of misconduct over the course of a season. All allegations are properly investigated. It is not uncommon for investigations to lead to no disciplinary charge being brought."
"The FA encourages all players who believe they have been either subject, or witness to, discriminatory abuse to report the matter immediately to the match officials on the day. Furthermore, all participants are advised to report any such alleged misconduct to The FA. In this case, the player and club were correct in reporting the matter to The FA and it was appropriate and proper for such an allegation to be thoroughly investigated."
The Metropolitan Police had begun investigating the alleged comments towards Chelsea's Mikel and Spanish team-mate Juan Mata, but soon dropped the case because of insufficient evidence.
This action led to Peter Herbert, chairman of the Society of Black Lawyers, accusing the FA of being "institutionally racist" for not doing enough to investigate the complaint.