Mourinho came onto the pitch to remonstrate with referee Chris Foy towards the end of their 1-0 defeat at Villa Park on 15 March.
The Chelsea boss requested a personal hearing with the FA on Wednesday but they decided to punish him for his actions.
Chelsea ended the match with only nine players after Willian and Ramires were sent off, with the second dismissal leading to the incident with Mourinho.
Ramires received a straight red for a two-footed challenge on Karim El Ahmadi, with Mourinho then coming onto the pitch to speak to Foy, who subsequently sent him to the stands.
"Chelsea manager Jose Mourinho has been fined £8,000 and warned as to his future conduct following an independent regulatory commission hearing," the FA statement read.
"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 has already been in trouble with the FA over a similar incident earlier in the season, when he was sent to the stands in the 4-1 home win Cardiff in October - the Portuguese accepted the charge and was also fined £8,000 on that occasion.
The defeat to Villa was the first of two straight losses on the road, with Chelsea going down 1-0 at Crystal Palace on 29 March, a result that led an angry Mourinho to declare his side were out of the title race.
"Can we play against Aston Villa again? No. The momentum was broken. Somebody broke the momentum," 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."