The Spanish Football Federation's Competition Committee announced the ban on Wednesday and said Simeone would be fined 3,005.00 euros ($3,399.86) and Atletico 1,050.00 euros.
Simeone was sent off at the end of the first half of Atletico's game with Malaga after a ball was thrown on to the pitch from the home side's technical area just as Malaga launched a counterattack nearby.
Simeone said the ball was thrown by one of the ball boys, although replays show the coach appearing to encourage the boy to toss the ball onto the pitch.
The Spanish Football Federation justified its ruling in a statement, applying law 101.2 of its disciplinary code which refers to "a grave altercation of the order of play".
The disciplinary code also states that "in a case where the suspect cannot be identified, the coach will be sent off for allowing an act which goes against the rules and will be sanctioned with a minimum of three games".
According to newspaper AS, Atletico President Enrique Cerezo said the club would appeal against the decision, which prohibits Simeone from taking charge of the team for the final matches against Rayo Vallecano, Levante and Celta Vigo. All three are crucial to Atletico's bid to win the La Liga title.
Atletico are second in the table, level on 82 points with leaders Barcelona, who are top because of their superior head-to-head record. ($1 = 0.8839 euros)