Matic was forced to withdraw from the Serbia squad earlier this month and missed his countries Nations League matches against Montenegro and Romania last week after suffering a back injury during United's dramatic 3-2 victory over Newcastle United.
The FA alleges Mourinho's language was "insulting and/or abusive and/or improper".
After the full time whistle blew, Mourinho was shown on TV cameras walking down the touchline and towards the tunnel at Old Trafford.
Second-half goals from Juan Mata, Anthony Martial and Alexis Sanchez ensured United avoided a fourth Premier League loss of the season and Mourinho spoke afterwards about the impact of "the pressure of man-hunting" on his players.
It is alleged the 55-year-old used "abusive, insulting or improper language" following United's 3-2 comeback win at Old Trafford.
He was reported to have said something in his native Portuguese language.
Ahead of Manchester United's clash against Newcastle United, reports emerged suggesting Jose Mourinho would be sacked regardless of the result. After facing Chelsea, United will have to face Juventus, who have a 100% win record this season, in the UEFA Champions League group stage game.