Portuguese defender Miguel Lopes opened the scoring for Akhisar Belediyespor, better known as Akhisarspor, with just over half an hour on the clock but Brazilian Fernandão equalised ten minutes after half time.
But rather than letting Fenerbahce surge ahead, Malian Abdoul Sissoko put Akhisar 2-1 up and Portuguese Helder Barbosa made it 3-1 just after 80 minutes.
Josef de Souza pulled the score back to 3-2 for Fenerbahce to create a nail-biting finale, but Akhisarspor held on after six minutes of injury time for a historic victory for their town in western Turkey’s Aegean region.
Fenerbahçe currently lie second in the Süper Lig behind Galatasaray with two weeks left of the season, but Akhisarspor are just above the relegation zone in 14th.
The final, the first match to be played in a new stadium in the New Diyarbakır Stadium in the Kurdish-majority city of Diyarbakır, had been overshadowed by controversy.
Fenerbahçe made the final after being awarded an automatic 3-0 walkover by the football authorities in the semifinal against Istanbul rivals Beşiktaş.
Beşiktaş refused to turn up to the resumption of a match called off after their head coach was hurt by an object thrown from the stands.
The opening of the 33,000 capacity stadium after three years of construction is seen as a major boost for the Kurdish-majority southeastern city.
Development of the Diyarbakır area has been held back due to the three-and-a-half decade insurgency of the outlawed Kurdistan Workers Party in the region.
Turkey has embarked on a massive spree of stadium building in recent years under President Recep Tayyip Erdoğan with new world-class stadiums in Antalya, Konya, Istanbul, and Trabzon opening in the last half decade.
Turkey is bidding to host the 2024 European football championships using the glitzy new stadiums, although Diyarbakır is not one of the proposed host cities.