Tuenday's ruling means Fenerbahce will be barred from next season's Champions League and Besiktas will miss out on the Europa League, reports Xinhua. Both bans were connected with match-fixing in domestic games in 2011.
The Istanbul-based Besiktas was summoned by the Control and Disciplinary Body of UEFA last week regarding charges first leveled against the club at the end of the 2010-11 season.
Actions against Besiktas was taken in relation to match-fixing activities which are alleged to have taken place during the 2011 Turkish Cup final.
The decision came as a shock for Turkish football as two giant clubs will not be able to represent the country in European competitions.