The under-pressure Chelsea boss, who was given the backing of the club in an official statement yesterday, was later charged by the FA over his comments about referee Robert Madley.
The Premier League champions lie 16th in the table after a poor run which saw them suffer a fourth defeat in eight games on Saturday.
In a statement on Monday, the FA said it had charged the Chelsea boss who was unhappy at the decision not to award a penalty when, with the scores at 1-1, forward Radamel Falcao was upended by Saints goalkeeper Maarten Stekelenburg.
The statement read: “José Mourinho has been charged for misconduct in relation to media comments he made following Chelsea’s game against Southampton on Saturday 3 October 2015.
“It is alleged his remarks constitute improper conduct in that they allege and/or imply bias on the part of a match official or match officials and/or bring the game into disrepute.
“He has until 6pm on Thursday 8 October 2015 to respond to the charge.”
Mourinho had said after the Southampton defeat: “When everything goes against you, you need these decisions. One thing teams are not afraid of is to make penalties against us because they make them all the time and the referees they never give.
“It is a big confidence they feel because they are not afraid to be aggressive in the box. I tell my players to be careful in the box. These opponents know that they don’t have to feel that pressure.”
Earlier on Monday Chelsea had expressed their confidence in Mourinho.
Following the 3-1 reverse, Mourinho said he would only quit if he lost the backing of the players, with club captain John Terry stating the dressing room remained firmly behind the Portuguese coach.
Chelsea took the unusual step of reiterating their backing in a statement on the official club website which read: “The club wants to make it clear that José continues to have our full support.
“As José has said himself, results have not been good enough and the team’s performances must improve.
“However, we believe that we have the right manager to turn this season around and that he has the squad with which to do it.”
Chelsea paraded the title and Capital One Cup through west London just five months ago, but are enduring their worst start to a season for 37 years.
Nevertheless, Monday’s statement indicates Abramovich has decided to stand by Mourinho, with a board meeting said to have been held following Saturday’s match at Stamford Bridge.
Mourinho enjoyed a highly successful first spell from June 2004 to September 2007 before returning in June 2013, and the former Real Madrid manager recently signed a new four-year deal worth around £8.5m (€11.5m) a season.
The 52-year-old, meanwhile, is adamant he will not be quitting.
Chelsea resume after the international break at home against Aston Villa, one of just four teams beneath them in the table, on October 17.