Fener's two-year ban remains but the suspended extra year has been removed from their punishment, while the Black Eagles are still disqualified from this year's Europa League
The sanctions were handed out last month as a result of a match-fixing scandal that occurred towards the end of the 2010-11 season.
Besiktas had their appeal denied while Fenerbahce’s two-year ban remains, but the five-year probationary period which could have resulted in an extra year’s suspension has been removed.
A Uefa statement read: “The UEFA Appeals Body carefully analysed the statements and documents submitted by Besiktas and Fenerbahce related to their specific cases, as well as the statements and documents submitted by the UEFA Disciplinary Inspectors appointed to each case, and reached the following decisions:
“Besiktas have had their appeal rejected. Consequently, Besiktas are not eligible to participate in the 2013/14 UEFA Europa League.
“Fenerbahce have had their appeal partially admitted. Consequently, Fenerbahce are excluded from participating in the next two UEFA club competitions they qualify for, including the 2013/14 Uefa Champions League.”
The clubs will now have the option to appeal the decisions of the Uefa Appeals Body to the Court of Arbitration for Sport.