Defender Gerard Pique (35), who was on the substitute bench, was given a four-game ban after he was shown a red card at halftime due to complaining to and insulting the referee in what was the last game of his career.
Lewandowski was shown a yellow card for dragging back Nacho Vidal in the 11th minute and 20 minutes later received his second after appearing to elbow David Garcia in the face.
According to the RFEF Officiating Committee, Lewandowski was given a three-game ban due to a gesture towards the official after he was shown the red card that was of "contemptuous attitude towards the referees".
It was only the second red card of Lewandowski's career, almost 10 years after he was sent off in the Bundesliga for Borussia Dortmund against Hamburg in February 2013.
The Polish striker will miss games against Espanyol, Atletico Madrid and Getafe when LaLiga resumes after the World Cup.
