Last season’s Champions League finalists were both suspended from signing new players until January 2018 after breaching rules regarding the protection of minors.
Fifa also confirmed Atletico had received a £696,000 fine, while Real Madrid must pay £278,000.
A Fifa statement read: “The FIFA Appeal Committee has decided to reject the appeals lodged by Spanish clubs Atlético de Madrid and Real Madrid and to confirm in their entirety the decisions rendered by the FIFA Disciplinary Committee in the respective cases relating to the protection of minors.
“As such, both clubs are to serve a transfer ban that prevents them from registering any players at national and international level for the next two complete and consecutive registration periods for breaching articles 5, 9, 19 and 19bis as well as annexes 2 and 3 of the Regulations on the Status and Transfer of Players (the “Regulations”).
“The transfer ban applies to each club as a whole — with the exception of the women’s, futsal and beach soccer teams – and does not prevent the release of players.
“Additionally, Atlético de Madrid and Real Madrid have been fined CHF 900,000 (£696,000) and CHF 360,000 (£278,000) respectively, while both clubs have been issued with a reprimand and a warning and given 90 days in which to regularise the situation of all minor players concerned.
“The grounds of the decisions taken by the FIFA Appeal Committee were communicated to the parties concerned today.
“For further information concerning the protection of minors, please read the FAQ document.”
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Real Madrid also reacted to the news with a statement of their own.
Theirs read: ” In light of today’s decision by the FIFA Appeal Committee, Real Madrid C. F. wishes to communicate the following:
“1. The club regrets said decision, understanding it to be deeply unjust and contrary to the fundamental principles of disciplinary law.
“2. The club will begin the appropriate appeals procedure before the Court of Arbitration for Sport (CAS), requesting that the decision be completely overturned, with absolute confidence that said organisation will come to an entirely favourable decision.
“3. Real Madrid C. F. will request that the procedure be undertaken in an urgent manner in order to obtain a decision from the CAS as quickly as possible.”
Real Madrid’s only summer business was to re-sign Alvaro Morata, while Atletico brought in Kevin Gameiro and Nico Gaitan as major transfers.