Mourinho was asked to leave the touchline by Craig Pawson during second-half injury time at St Mary's on Saturday, after fourth official Mike Jones pulled him back for encroaching on to the edge of the pitch.
Speaking after the game, Mourinho was none the wiser over the referee's decision.
"I don't know [what happened]," he said. "Craig told me to leave, and I left."
The FA have confirmed that, whatever Mourinho's offence, it did not warrant further punishment and he will be free to take his place in the Old Trafford dugout when United host struggling Crystal Palace next weekend.
Mourinho was sent to the stands by Mark Clattenburg during a 0-0 home draw with Burnley, having already been charged with misconduct with regards to comments made about referee Anthony Taylor before United's trip to Anfield to face Liverpool.