The FA have decided there is "no case to answer" over the allegation the referee said "shut up you monkey" to midfielder John Obi Mikel.
An FA statement also said the complaint by Mikel's team-mate Ramires was "made in good faith".
Clattenburg spoke of his relief and said the last few weeks had been "the most stressful of his life".
He said: "I am looking forward to putting this behind me and concentrating on refereeing in the Premier League and other competitions.
"I am extremely grateful for the invaluable support of my family, my Select Group colleagues, the management of Professional Game Match Officials Limited and our union Prospect. The messages of encouragement from those inside and outside of the game have helped me through the most stressful time of my professional life.
"To know you were innocent of something but that there was the opportunity for it to wreck your career was truly frightening.
"Racism has no place in football and this experience should not discourage those to speak out if they genuinely believe they are a victim of abuse. However, there are processes that should be adhered in order that any investigation can be carried out in a manner that is fair for all parties involved.
"I know first-hand the ramifications of allegations of this nature being placed into the public domain ahead of a formal process and investigation. I hope no referee has to go through this in the future."
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The FA said 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.
An 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."
Mikel meanwhile has now been charged by the FA for using threatening words or behaviour - an alleged breach of FA Rule E3 - after going into the referees' changing room after the match in question - Chelsea's 3-2 defeat by Manchester United at Stamford Bridge on October 28.
An FA statement said; "It is alleged that in or around the Match Officials' changing room at the end of the fixture, Mikel used threatening and/or abusive and/or insulting words and/or behaviour.
"The player has until Friday 30 November 2012 to respond to the charge."
Referees chief Mike Riley said they will look to record all match officials' conversations during games in the future.
Chelsea said they had had a duty to report the claim against Clattenburg.
A club statement said: "Chelsea Football Club accepts the Football Association's decision regarding Mark Clattenburg and welcomes the fact that the FA recognises the club and players were correct in reporting the matter.
"The FA states Chelsea took the correct action following the Manchester United match and 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, and in turn to the FA.
"The club also notes the charge brought against John Mikel Obi. While the player does not deny the charge, he will request a personal hearing to explain the mitigating circumstances.
"With regards to the Mark Clattenburg decision, the club accepts the case is now concluded and notes the FA states the allegation was made in good faith."