Reigning cup champions Barcelona beat Levante 4-2 on aggregate but played defender Chumi in their 2-1 first leg defeat, despite the player being suspended for Barcelona B at the time.
The Spanish football federation (RFEF) rejected Levante's complaint, however, because it arrived after the 48-hour deadline following the first leg match on Jan. 10.
Levante appealed the decision and after that was rejected on Monday the club turned to CAS, asking for the suspension of the tournament until the issue is resolved.
"Levante will present their case to the Court of Arbitration for Sport after the RFEF appeal committee rejected the complaint over an ineligible line up from Barcelona," Levante said on Twitter late on Monday, with Spanish reports confirming they had filed the paperwork on Tuesday.
Getafe are due to host Valencia on Tuesday in the first quarter-final - which is set to go ahead - with Barcelona travelling to face Sevilla on Wednesday.
Barcelona believe they were able to play Chumi as minor suspensions are usually served in the division in which they are picked up.
(Reporting by Rik Sharma; Editing by Hugh Lawson)
