Pachuca Group owns the two Mexican clubs, but has claimed that the associations are run independently of each other.
The International Football Federation (Fifa) disagrees and now León will not be allowed to play the Club World Championship this summer. Only Pachuca will get a spot in the 32-team tournament, which will be played in several American cities from June 15 to July 13.
The ownership group will appeal to the Sports Arbitration Court (Cas).
The issue of the Mexican clubs' participation came to the table after Costa Rican club Alajuelense questioned their right to play the tournament.
Which club will replace León will be announced by Fifa at a later time. The team was drawn to play in a group with Flamengo (Brazil), Esperance Tunis (Tunisia), and Chelsea (England).
