Levante said that Barca had played defender Juan ‘Chumi’ Brandariz in last week's Copa del Rey last-16, first-leg game, which Levante won 2-1, when he was supposed to be serving a suspension.
A statement from the federation said the head of the competition, Carmen Perez, had rejected Levante's complaint because it arrived after the 48-hour deadline.
"After studying the complaint and the corresponding allegations, the head of the competition has decided to maintain the result of the tie and keep Barcelona in the quarter-final draw," the federation said.
Levante said in a statement that they will appeal the decision.
Barca, who have won the last four editions of the Copa del Rey and have lifted the trophy a record 30 times, won Thursday's second leg 3-0 at the Nou Camp for a 4-2 aggregate win.
Ernesto Valverde's side will face Sevilla, who they thrashed 5-0 in last year's final, in the quarter-finals following the draw, which was made shortly after the federation announced it had rejected Levante's complaint.
The federation's decision means Barca escape the fate of Real Madrid, who were thrown out of the 2015-16 Copa del Rey for playing Denis Cheryshev in a last-32 game against Cadiz when he was supposed to be serving a suspension from the previous season when he played for Villarreal.
(Reporting by Richard Martin; Editing by Toby Davis)
