The suspension was confirmed by the Spanish Football Federation on Wednesday after Simeone was sent to the stands at half-time in the Malaga game by referee Antonio Mateu Lahoz.
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The extra ball was thrown onto the pitch from near the Atletico bench by a ball boy, in what appeared to be a case of gamesmanship.
Spanish federation rules stipulate that as the culprit couldn't be identified at the time by the referee, Simeone is held responsible as the most senior figure on the bench.
The Argentine will though be free to sit on the bench for Atletico's Champions League semi-final, first leg against Bayern Munich later on Wednesday.
"It is clear the referee took the correct decision," Simeone said after Saturday's match.
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The news is a big blow to Atletico's title hopes as they lie second in the table behind Barcelona only due to their inferior head-to-head record.
Simeone will miss home games against Rayo Vallecano and Celta Vigo as well as the trip to Levante.
Atletico have 10 days to launch an appeal.
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