The Turkey-France co-production depicts the volatile relationship between a professor and his young girlfriend.
Other winners in the 12-film competition line-up included Bosnian drama Skies Above The Landscape which won the best director prize and $16,544 (Y2m) for helmer Nenad Djuric.
Best screenplay went to Manuela Stacke's Children Of The Moon while the Best Technology prize was awarded to Danish fantasy Skymaster - A Flying Family Fairytale, directed by Michael Wikke and Steen Rasmussen. Angus Gibson's South African drama Heartlines won the Special Jury Prize.
In the Japanese short film category, Atsushi Suzuki's animated Let's Go Bang-Chow Dead Or Alive won best picture, while Bunji Sotoyama's Stardust Serenades and Tazuko Aso and Tetsuya Kawaguchi's Twilight Clouds - First Love won honorable mentions.
This year's jury was headed by Hong Kong director Mabel Cheung and included screenwriter Coleman Hough (Bubble), Japanese producer Akira Morishige (Vibrator) and Dutch film critic Peter van Bueren.
Established in 2004 and focusing exclusively on digital cinema, Skip City is held in Saitama Prefecture 's Kawaguchi City, neighbouring Tokyo.