World football's governing body suspended the two La Liga clubs from doing business for two transfer windows back in January, although the bans were temporarily lifted after the Madrid neighbours both contested the ruling.
However, FIFA announced on Thursday that Los Blancos and Los Rojiblancos will be blocked from strengthening their respective squads for the next two transfer periods after failing with their appeals.
They will be allowed to operate in the January 2018 transfer window, although the Spanish pair are now expected to take their cases to the Court of Arbitration for Sport (CAS).
"The FIFA Appeal Committee has decided to reject the appeals lodged by Spanish clubs Atletico 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," read a statement from FIFA.
"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 and CHF 360,000 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."