A UEFA appeals panel upheld a disciplinary verdict that officials of the Istanbul club helped fix matches during their 2010-11 league title run.
However Fenerbahce, who were also barred from the Champions League two years ago, have the option of challenging the UEFA verdict at the Court of Arbitration for Sport.
Club officials, including president Aziz Yildirim, deny wrongdoing and are appealing their criminal convictions in Turkish courts.
Fener had been excluded from competing in continental competition for three seasons in total, with the third deferred for a probationary period of five years, but that final year of exclusion has now been dropped altogether.
They finished second in the league last season and would have been eligible to enter the Champions League third qualifying round.
Third-placed Besiktas would have been in line to claim the vacant Champions League spot but they have had an appeal against fixing the 2011 Turkish Cup final dismissed.
Fourth-placed Bursaspor will therefore enter the draw on Friday.