The Spaniards were given the 14-month ban after being found to have breached rules on signing international players under the age of 18.
It was suspended after they appealed, allowing them to sign Luis Suarez.
Barcelona will now take the case to the Court of Arbitration for Sport (Cas).
The ban will start in the next transfer window, early next year, which means their summer acquisitions will be unaffected.
And the Catalan club could, if they wanted, sign more players before the current transfer window ends on 31 August.
In a statement, the club said it would "continue defending its interests before the highest sporting authority, in this case the Court of Arbitration for Sport".
Barcelona added that the punishment was an "affront to the spirit" of their "world renowned" academy La Masia, which is regarded as being the foundation of
the club's success in recent years.
Players are instilled with a philosophy of how the game should be played and many of the first team, such as Lionel Messi, Andres Iniesta and Xavi Hernandez, have graduated from the academy which
is situated near the Nou Camp.
"FC Barcelona is to serve a transfer ban which will see the club prevented from registering any players at both national and international level for two complete and consecutive transfer periods," read a Fifa statement.
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