Lewandowski, 34, was due to miss the game as the first of a three-match suspension but a Spanish court on Friday placed the ban on hold until Barca receive a final resolution to an appeal they lodged in December.
The Poland striker played all 90 minutes of the fixture at Camp Nou, which ended 1-1 and saw both sides end the game with 10 men after a fiery second half.
“Espanyol have submitted a written complaint to the Royal Spanish Football Federation (RFEF) against Barcelona for fielding an incorrect line-up,” a statement from the LaLiga side said on Monday.
“Before the start of the match, the club notified the match referee, Mateu Lahoz, and the RFEF about the presence of Lewandowski, who should have been fulfilling a suspension after his dismissal in the previous league game.
“We will use all the resources we have to defend the club’s interests. This flagrant injustice poses a risk to the essence of the competition and is based on a hasty resolution and clear legal mishaps.”
Per the RFEF’s rules, fielding an ineligible lineup could result in the three points being awarded to the other team in addition to a fine.
Barca will argue Lewandowski was available for selection after revealing on Friday that a “dispute settlement court in Madrid issued a precautionary measure against the suspension imposed by the Court of Arbitration for Sport.”
Lewandowski was sent off for two bookable offences against Osasuna in November, for which he received a one-game ban. He was handed an additional two-match suspension for a gesture made towards the referee as he left the pitch.
Barca appealed the sanction, saying the gesture was for coach Xavi Hernandez, not the referee.
Meanwhile, Barca are still waiting for the final outcome of their appeal. They travel to Atletico Madrid in LaLiga on Sunday and don’t yet know if, when or how many games Lewandowski will sit out.
After drawing with Espanyol, they remain top of LaLiga but are now level on points with Real Madrid.