The game between two of the country's biggest teams was abandoned after 57 minutes after the Besiktas coach was hit on the head by an object thrown by Fenerbahce fans.
The Turkish football federation ruled that the last 32 minutes of the match should be completed on May 3 behind closed doors.
Besiktas said they had received the federation's decision with sadness and dismay.
"We have been on the field for 115 years, we have won, had draws or lost on the field. In order not to accept being losers, we will not show up on the field on May 3," Besiktas said in a statement on their website.
The match was level at 0-0 when it was abandoned and the first leg was drawn 2-2.
(Writing by Ezgi Erkoyun, editing by Ed Osmond)
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