Besiktas have been refused entry into the cup next season and will pay back the 4 million Turkish lira (around £690,000) they earned from the competition this campaign as a result of their absence.
Because Besiktas didn't turn up, Fenerbahce had a light training session on the Şükrü Saracoğlu Stadium pitch instead.
The second leg on April 19 was stopped in the 57th minute after Besiktas coach Senol Gunes was struck by an object thrown by a Fenerbahce fan in the stands. He needed five stitches in his head after he was rushed to hospital with the tie poised at 2-2.
The remainder of the fixture was scheduled, by the Turkish Football Federation (TFF), to be played behind closed doors on May 3 – but Besiktas made clear last week that they didn't want to take any part in the shortened game.
"We have been on the field for 115 years; we have won, had draws or lost on the field. In order not to accept losing to backstage football politics, we will not show up," Besiktas said in an official club statement last week.
Shortly before the match was abandoned, Besiktas had Pepe sent off so would have had to play the remainder of the game with 10 men.
Once it became blatantly obvious that Besiktas weren't showing up, Fenerbahce coach Aykut Kocaman told reporters: "Besiktas made a difficult decision. I would have preferred to lose instead of winning this way."
Fenerbahce will now play Akhisarspor in the cup final on May 9.
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