The Portuguese, who was also fined 16,000 pounds ($19,982), was banished from the dugout in the 27th minute of Sunday's 1-1 home Premier League draw with West Ham United after kicking a water bottle down the touchline following a booking for midfielder Paul Pogba that he felt was unjust.
“Following an Independent Regulatory Commission hearing today... Jose Mourinho will serve a one-match touchline ban with immediate effect,” the FA said in a statement.
“The Manchester United manager admitted an FA charge that his behaviour in or around the 27th minute of the game against West Ham United on Sunday... amounted to improper conduct.”
Mourinho was also dismissed for verbally abusing referee Mark Clattenburg at halftime during a match against Burnley at the end of last month.
The former Chelsea, Real Madrid, Inter Milan and Porto boss was banned from the touchline for one match and fined a total of 58,000 pounds ($71,972) for two separate incidents of misconduct in October.
He admitted using abusive and/or insulting language towards Clattenburg and was fined 8,000 pounds for the incident and banned from the touchline for one game.
Mourinho was also charged and fined a further 50,000 pounds for comments he made about referee Anthony Taylor ahead of a game against Liverpool.
United are sixth in the Premier League with 20 points from 13 matches, 11 adrift of leaders Chelsea.
Mourinho's team entertain West Ham again in the League Cup quarter-finals on Wednesday.
Original source: Mourinho handed second touchline ban for the season