Silva's intended move from Portuguese side Sporting to English Premier League club Leicester was blocked by FIFA because it fell outside the registration period, CAS said.
Leicester bought the 28-year-old just before the transfer window closed on Aug. 31, but FIFA, which handles international transfers, received the paperwork moments after the deadline for registration ended.
Silva appealed to CAS, sport's highest tribunal, against the decision and also applied for "urgent provisional measures" which would allow him to register for Leicester until the final appeal was heard.
CAS said in a statement that it had rejected the application for provisional measures, but the proceedings would continue "and a final decision on the merits will be issued after a hearing, which is yet to be fixed".
(Writing by Brian Homewood in Berne; Editing by Toby Davis)
