Levante initially filed a complaint on Friday over Barca defender Chumi, who played in the first leg of the clubs' last-16 tie last Thursday.
The game, which Levante won 2-1, featured the defender, who was set to serve a suspension with Barcelona B the following weekend.
Because of Chumi's participation in the match, Levante argued that Barcelona should have been disqualified from the tournament due to fielding an ineligible player .
Judge Carmen Perez, however, declared Levante's complaint to be filed too late on Friday, after Barca defeated the Valencia-based side 3-0 in the return leg on Thursday to advance to the competition's last eight.
"The sole judge of Competition, Carmen Perez, considers in accordance with the regulations in effect in the RFEF that the complaint presented by Levante UD at 9:33 am on this Friday has been received outside the established deadline," a statement from the Spanish Football Federation (RFEF) read on Friday.
"Once the complaint and the corresponding allegations have been studied, the single judge of Competition has decided to maintain the result of the tie and keep FC Barcelona in the draw for the quarter-finals of this afternoon for the reasons previously stated."
That draw took place on Friday, and Barcelona were paired with Sevilla in a rematch of last season's final.
Barcelona are looking to win the competition for the fifth consecutive season.
Full quarter-final draw (ties to take place over two legs)
Real Madrid vs Girona
Getafe vs Valencia
Sevilla vs Barcelona
Espanyol vs Real Betis