The Portuguese claimed the Premier League leaders were the victim of a "campaign" to influence referees after Anthony Taylor booked Cesc Fabregas for diving when the Spain midfielder was brought down by Matt Targett in the penalty area.
Mourinho was charged by the FA earlier this month as a result of those accusations and the former Real Madrid coach has now been hit in the pocket by the governing body.
A statement on the FA's official website said: "Following an Independent Regulatory Commission hearing, Jose Mourinho has been fined £25,000 after he was found to have breached FA Rules in relation to media comments.
"The Chelsea manager denied that comments he made after the game against Southampton on 28 December 2014 constituted improper conduct in that they alleged and/or implied bias on the part of a referee or referees, and/or brought the game into disrepute.
"The Independent Regulatory Commission found the comments were a breach of FA Rule E3 in that they were improper and brought the game into disrepute. The Commission did not, however, find that the comments implied bias on the part of a referee or referees.
"Mr Mourinho, who had requested a non-personal hearing, was also warned as to his future conduct."
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