UEFA has banned the club - who were due to enter in the third qualifying round of the Champions League - from European football for three seasons in total, although the ban for the third season in which they qualify is deferred for a probationary period of five years.
Fellow Turkish outfit Besiktas have been suspended for one season by UEFA's Control and Disciplinary Body (CDB), meaning they will be barred from next term's Europa League.
Both bans are connected with match-fixing in domestic games in 2011 and it is Fenerbahce's second exclusion from Europe's top competition after they were withdrawn from the 2011/12 Champions League by the Turkish Football Federation when the scandal broke.
Fenerbahce won the Turkish title in the 2010/11 season with a 4-3 win over Sivasspor in their last match, which was one of around a dozen games investigated by the TFF.
UEFA said before the hearing that the Besiktas case involved the 2011 Turkish Cup final where they beat Buyuksehir Belediyespor on penalties after a 2-2 draw.
The European governing body also imposed a suspended one-year ban from European competition on Romanian side Steaua Bucharest, who were accused of a breach of Champions League participation regulations.
Fenerbahce have said they will appeal the decision, with the other two entitled to do so.