The Istanbul club were booted out of the competition due to financial irregularities, but had hoped to have the decision overturned by the international body
It was announced in May that the Istanbul club would be excluded from the next two Uefa competitions for which they qualified due to financial misdemeanours, along with Gaziantepspor and Bursaspor.
Upon appeal, Bursaspor were reinstated to the former Uefa Cup, but Besiktas' bid to be get their place in the tournament back has been thrown out after a hearing in Lausanne on July 5.
"Besiktas are excluded from the next two Uefa club competitions for which it qualifies in the next five seasons," an official CAS statement confirmed.
"The exclusion for the second competition is suspended for a probationary period of five years. Besiktas are fined €200,000, of which €100,000 is suspended for a probationary period of five years."
Besiktas had finished fourth in the Turkish Super Lig, which would have granted them a place in the qualifying rounds for the competition.
In the previous edition of the Europa League, the Inonu club were knocked out by eventual winners Atletico Madrid at the last-16 stage.
Eskisehirspor will take their place in the upcoming season's competition.