The Catalan giants announced soon after the verdict that they would take their case to the Court of Arbitration for Sport (CAS).
Barca are still able to make signings during the current window, which closes on September 1, but will then have to wait until January 2016 to engage in any further incoming transfer activity.
They were initially hit with a ban – lasting two transfer windows – in April after irregularities were found in their dealings at youth level.
The sanction came after FIFA ruled that the club had breached rules in the signing of 10 players under the age of 18 between 2009 and 2013.
Barca were successful in getting the transfer ban suspended, though, pending the outcome of an appeal.
And that has allowed them to bring the likes of Luis Suarez, Jeremy Mathieu, Ivan Rakitic, Marc-Andre ter Stegen, Claudio Bravo and Thomas Vermaelen to the club in recent months.
FIFA, who also sanctioned the Spanish Football Federation for violating their rules, announced its final judgement on the matter on Wednesday, confirming that the club's appeal had been thrown out.
A statement from the governing body read: "The FIFA appeal committee has decided to reject the appeals lodged by Spanish club FC Barcelona and the [Spanish Football Federation] Real Federacion Espanola de Futbol [RFEF] 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, 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, starting with the next registration period (January 2015) given that the appeal of the club had been granted suspensive effect by the chairman of the FIFA Appeal Committee.
"FC Barcelona has also been ordered to pay a fine of CHF 450,000 [€371,000] and been given a period of 90 days from today in which to regularise the situation of all minor players concerned.
"Meanwhile, the RFEF has been ordered to pay a fine of CHF 500,000 [€412,000] and granted a period of one year in which to regularise their regulatory framework and existing system concerning the international transfer of minors in football.
"The terms of the decisions taken by the FIFA Appeal Committee were communicated to FC Barcelona and the RFEF today."
Barca said of FIFA's decision: "FC Barcelona may not in any way share a resolution that is an affront to the spirit of our Masia, a world renowned example of academic, human and sporting education."