Lewandowski was hit with a suspension after a red card against Osasuna in November before the World Cup break.
The decision to suspend his ban meant the Polish forward, La Liga's top goalscorer could play in the Catalan derby on 31 December, but he failed to score in the 1-1 draw.
Espanyol were angered by the court decision and their president and board refused to attend the match against Barcelona.
Lewandowski will now miss the league leaders' fixtures against Atletico, Getafe and Girona.
The former Bayern Munich striker had two additional matches added to his automatic one-match suspension for dismissal against Osasuna, after making a gesture perceived as disrespectful towards the referee.