Leicester had agreed a £22m deal for the 28-year-old Portuguese international as the transfer window loomed.
The decision means that Leicester cannot register the player, despite owning him, until the transfer window opens again in January. The club are appealing to try and register the player for the first half of the season.
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Sporting President Bruno de Carvalho adwas sympathetic, saying: "The transfer of Adrien is already completed. Hopefully Leicester find a solution for him."
Silva was purchased to replace Danny Drinkwater, who was sold to Chelsea for £35 on the same day.
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