Brazilian midfielder Ramires has been charged with violent conduct for swinging his forearm at Sebastian Larsson and is now likely to miss the club's final three games of the Premier League season.
Assistant coach Faria, meanwhile, is hit with two counts of misconduct.
The Portuguese was furious with referee Mike Dean for awarding the Black Cats the penalty that won them the game in the 82nd minute.
He has been charged with using abusive and/or insulting words towards the official and also acting aggressively enough to be sent off.
Ramires has until 6pm tomorrow to respond to the charge, while Mourinho and Faria have until 6pm Monday.
The defeat was Mourinho's first in a league game at home with Chelsea, ending a 77-game unbeaten streak at Stamford Bridge.