Mourinho requested a personal hearing following an improper conduct charge after he was sent to the stands by referee Chris Foy towards the end of a 1-0 loss at Villa Park.
A FA statement read: "Chelsea manager Jose Mourinho has been fined £8,000 and warned as to his future conduct following an independent regulatory commission hearing.
"Mourinho denied a breach of FA rule E3 in that his behaviour in re-entering the field of play and approaching the match referee (Foy) in an attempt to speak to him, in or around the 90th minute of the game against Aston Villa on March 15, 2014, amounted to improper conduct.
"However, the charge was found proven at a personal hearing on Wednesday, April 9."
Mourinho, who on Tuesday guided Chelsea into the Champions League semi-finals, has been seething since the loss at Villa, the first of two away defeats in succession in the Premier League.
After the second, at Crystal Palace, Mourinho conceded Chelsea's title chances were over, although they are two points behind leaders Liverpool entering this weekend's fixtures.
Mourinho said recently: "Can we play against Aston Villa again? No.
"The momentum was broken. Somebody broke the momentum."
Mourinho also believes Foy's performance could prove costly for Chelsea.
He said: "The other matches we lost because we didn't play well. You find the natural reasons for losing a match.
"If you go to the Villa match it's difficult. What happened in the defeat against Villa I never learn, I never accept.
"Somebody was very successful in putting a hurdle in front of us. And we crashed the hurdle against Aston Villa and we lost.
"Villa was not a normal football match and we always hope that football matches are normal."
It was the second time Mourinho had been sent to the stands this season.
Following his sending off against Cardiff in October, Mourinho accepted the charge and was fined £8,000.
Chelsea lost 1-0 at Villa Park, with Mourinho dismissed after Ramires had been shown a red card for an over-the-top tackle on Karim El Ahmadi. As well as Ramires, Willian was sent off during the contest.
The Chelsea manager came on to the pitch as a melee ensued involving players from both teams, with the substituted Gabriel Agbonlahor and Villa manager Paul Lambert also on the pitch.
The Portuguese claimed he was only attempting to cool tempers and to ask Foy why he had not sent off Agbonlahor for accosting Ramires, but the referee was not interested and he dismissed the Chelsea manager.
Mourinho then asked to speak to Foy in the referee's room, but he did not want to speak to the Chelsea boss.
The Blues boss then called on the Premier League not to appoint Foy for Chelsea matches.
Mourinho also left his technical area after Demba Ba's decisive strike against Paris St Germain on Tuesday, racing down the touchline in celebration and to provide tactical instructions.
The Portuguese has avoided punishment from UEFA, though.
UEFA said: "No disciplinary proceedings have been opened in this regard."