The Europa League semi-finalists have been slapped with a two-year ban from continental competition, while the Black Eagles are excluded from next season's Europa League
Both Istanbul giants were embroiled in a match-fixing scandal at the tail-end of the 2010-11 campaign which saw Aykut Kocaman's side's miraculous run to the Super Lig title subject to suspicion.
Besiktas, meanwhile, won the Turkish cup that year on penalties against Istanbul BB, but they soon gave back the trophy when the investigation was announced.
A statement released on Uefa's official website read: "The Uefa Control and Disciplinary Body (CDB) today announced its decisions following the disciplinary proceedings relating to Fenerbahce SK (Turkey), Besiktas JK (Turkey), and FC Steaua Bucuresti (Romania).
The CDB carefully analysed the situation of both Fenerbahçe SK and Beşiktaş JK and has pronounced the following sanctions:
• Besiktas JK is not eligible to participate in the 2013/14 Uefa Europa League.
• Fenerbahce SK is excluded from participating in the next three Uefa club competitions for which it would qualify, including the 2013/14 Uefa Champions League season. The ban for the third season is deferred for a probationary period of five years."
Steaua Bucharest have also been handed a one-year suspension from competing in Uefa competitions, though this has been deferred for five years.
Fener had been due to compete in the Champions League this term after finishing second in the league, with Besiktas coming third.
However, Uefa has exercised its right to ban Fenerbahce for two years, with a further campaign suspended, while Besiktas are to miss one year of continental football.
The Black Eagles also missed the Europa League last term after failing to meet financial requirements.