The Istanbul giant had appealed UEFA's initial two-year ban with CAS and was consequently allowed to take part in the qualification phase of the Champions League where the team was beaten 5-0 on aggregate by Arsenal, provisionally seeing it enter the group phase of the Europa League.
However, CAS has now made the decision to turn down Fenerbahce's appeal, meaning that the club will be banned from playing European football for 2013-14 and 2014-15.
"CAS has dismissed the appeal filed by Fenerbahce against the decision taken by UEFA to exclude them from European club competitions," an official CAS statement reads.
"UEFA excluded Fenerbahce from the UEFA club competitions for two seasons because of match fixing. The Turkish club appealed such decision to the CAS and in agreement with the parties the CAS established an expedited procedural timetable and granted a stay of the UEFA decision to the Turkish club, allowing it to take part in the qualification phase of the current edition of the Champions League until the outcome of the CAS appeal was known.
"Pursuant to the UEFA decision, which is now confirmed by the CAS, Fenerbahce are excluded from two editions of the UEFA club competitions."
Meanwhile, CAS has also rejected Metalist Kharkiv's appeal against a one-year ban from European football.
The Ukrainian side was suspended due to its role in a match-fixing scandal as well, and had already been disqualified from the Champions League playoffs as a result, with PAOK taking the vacated spot.
"CAS has dismissed the appeal filed by Metalist Kharkiv against the decision taken by UEFA to exclude them from European club competitions," the statement continued.
"Pursuant to the UEFA decision, which is now confirmed by the CAS, Metalist Kharkiv are excluded from the UEFA club competitions 2013-14."
UEFA has welcome CAS' decisions to reject Fenerbahce and Metalist's appeals and will meet later on Thursday to determine what will happen to the Turkish giant's Europa League place.
"UEFA welcomes today's decisions of CAS rejecting the appeals made by Fenerbahçe and Metalist Kharkiv against the UEFA Appeals Body decisions of 15 July 2013 and 14 August 2013 respectively," UEFA's statement read.
Fenerbahce has made an official announcement indicating that the club will continue the judicial procedure. The Turkish club underlines that it will appeal to the Swiss Federal Court about the decisions made by the UEFA and CAS.