Fans threw flares, litter and a knife onto the pitch and tore down the stadium's security netting as the match ended after a 90th minute penalty for Konyaspor in the Black Sea city of Samsun.
Supporters of Atiker Konyaspor, the main team from Turkey's central Anatolian province of Konya, chanted slogans accusing Besiktas and its fans of links to the Kurdistan Workers Party (PKK), which has waged a three-decade insurgency against the state.
Fans of Besiktas, an Istanbul side whose supporters include a vocal leftist element, responded with a song popular among secular Turks, aimed at the rival fans from Turkey's conservative heartland. The two groups rushed onto the field and fought after the final whistle.
The interior ministry, investigating the clash, said it would ensure that security measures were tightened. Both teams were under review for possible disciplinary action from the Turkish Football Federation, the Hurriyet newspaper said.
Last season, Atiker Konyaspor won their first ever Turkish Cup in the first final since the 2007-08 season in which none of Istanbul's "big three" clubs - Besiktas, Fenerbahce and Galatasaray - were competing.
Besiktas, meanwhile, won their second consecutive Turkish league title, and the 15th in their history, last season.
(Reporting by Tuvan Gumrukcu and Dirimcan Barut; Editing by David Dolan and Andrew Bolton)
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