Lewandowski was dismissed for two bookable offences in Barca's final game before the World Cup break in November – a 2-1 win at Osasuna.
The Spanish Football Federation (RFEF) initially hit Lewandowski with an extended three-match ban due to an alleged gesture he made towards referee Jesus Gil Manzano, but his punishment was put on hold last week following a complaint to the Court of Arbitration for Sport.
Lewandowski was therefore able to play in Saturday's 1-1 draw at Camp Nou – an ill-tempered affair in which referee Antonio Mateu Lahoz showed 17 yellow cards, including one for Barca coach Xavi, sending off Jordi Alba and Vinicius Souza.
Despite claiming a valuable point in their bid to avoid relegation, Espanyol has challenged the eligibility of Lewandowski to play.
A statement on the club's website read: "RCD Espanyol has submitted a letter of complaint to the Royal Federation of Spanish Football (RFEF) to challenge the match against FC Barcelona for improper alignment.
"Before the start of the match, the club notified in good faith the referee Antonio Mateu Lahoz, like the RFEF itself, about the presence in the rival eleven of Robert Lewandowski, who had to serve a penalty after his expulsion for a double yellow in the previous game of the championship.
"RCD Espanyol, as announced on the eve of the match, will use all the resources at its disposal to defend its interests and those of our fans, aware that this flagrant injustice puts the essence of our competition at risk, and that this injustice it is based on a hasty resolution with obvious legal deficiencies."
Lewandowski failed to find the net against Diego Martinez's men, though he was involved in one notable incident when Leandro Cabrera was shown a red card for appearing to stamp on the striker – though Lahoz reversed the decision following a VAR check.
Any ban for Lewandowski would represent a severe blow for Barca, with the Poland striker scoring 13 goals in 15 LaLiga appearances.
Barca visits third-tier side Intercity in the Copa del Rey on Thursday, before facing Atletico Madrid in LaLiga and taking on Real Betis in the Supercopa de Espana semi-finals.