The Blues boss and his assistant are accused of misconduct while the Brazilian midfielder may miss the rest of the Premier League season for appearing to strike Sebastian Larsson.
"Congratulations to Mike Dean because he made a fantastic performance," the Portuguese sarcastically told the press, "and congratulations to Mike Riley because what they did during the season was fantastic for the way the championship is going."
Faria had to be held back by fellow Blues staff as he fumed at the penalty that won Sunderland the game and is hit with two misconduct charges, one for abusive language and the other for improper conduct.
Ramires, meanwhile, is charged with violent conduct and faces a retrospective red card and a four-match ban that would end his season, with the standard three amplified by one for it being his second dismissal of the campaign.
The Brazilian appeared to strike Sebastian Larsson in the face in the first half at Stamford Bridge and has until Thursday evening to respond to the charge.
Mourinho and Faria have until Monday to decide on their responses.