The match at New Konya Stadium saw last season's Ziraat Turkish Cup winner Akhisarspor pitted against league champs Galatasaray.
Akhisarspor took the lead early as Ukrainian forward Yevhen Seleznyov scored in the fifth minute.
Galatasaray managed to equalize the match at 1-1 in the 79th minute with striker Eren Derdiyok.
Regular time and extra time both ended with a 1-1 draw as teams advanced to a penalty shootout.
In the shootout, Akhisarspor made no mistake in their five attempts.
However, Galatasaray's striker Bafetimbi Gomis missed the last penalty, meaning Akhisarspor won the cup.
The Video Assistant Referee (VAR) system was also used for the first time in an official match in Turkey.