Mourinho was punished for saying referees were afraid to award penalties to the Premier League champions after Chelsea's 3-1 home defeat by Southampton on Oct. 3.
"The appeal board has upheld the original sanction and therefore it remains that Mr Mourinho's suspended stadium ban will be immediately invoked should he be found by an Independent Regulatory Commission to have committed (a similar offence in the next 12 months)," the FA said in a statement.
The punishment is separate from the immediate one-match stadium ban and 40,000 pounds fine Mourinho received for misconduct during the 2-1 defeat by West Ham United on Oct. 24.
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The Portuguese, sent to the stands at Upton Park after trying to speak to referee Jon Moss at halftime following Nemanja Matic's red card, will miss Saturday's trip to Stoke City who knocked Chelsea out of the League Cup last week.
It has been a turbulent few weeks for Mourinho whose Chelsea side are struggling near the foot of the Premier League table having endured a miserable start to the season.
He has also been named as a respondent in the legal action being brought against the club by former team doctor Eva Carneiro for constructive dismissal, sources close to the case who declined to be identified said on Monday.
There was some good news for Mourinho on Wednesday when Chelsea beat Dynamo Kiev 2-1 at Stamford Bridge to climb to second place in their Champions League group with two matches to play.
(Reporting by Toby Davis; Editing by Tony Jimenez)
