The Spanish football federation says the suspension will be served next season since Atletico was eliminated on Tuesday.
Simeone was sent off during Tuesday's 3-1 cup loss to Sevilla for protesting a decision by the referee, earning a one-match touchline ban.
The punishment was extended by two matches because Simeone applauded the referee in a mocking fashion when he was dismissed.
Atletico was eliminated 5-2 on aggregate in the two- legged quarterfinal.