Television cameras captured Mourinho muttering what are purported to have been "abusive and/or insulting and/or improper" remarks.
The United manager had been the subject of intense speculation in the build-up to the stirring late 3-2 victory, with a report in The Mirror claiming he would be sacked regardless of the result.
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.
But it is his touchline comments that have brought the under-pressure manager to the FA's attention.
"Jose Mourinho has been charged following Manchester United's game against Newcastle United on October 6, 2018," read an FA statement.
"It is alleged that his language at the end of the fixture, as captured by the broadcast footage, was abusive and/or insulting and/or improper."
Mourinho has until 18:00 local time (17:00 GMT) on October 19 to respond to the charge.