Bosnian defender Safet Nadarevic was sent off ten minutes after the restart for a second bookable offense but Eskisehirspor still managed to cause an upset.
Guinean striker Souleymane Youla scored the precious winner nine minutes past the hour mark after a neatly-worked counter attack.
Egyptian defender Al-Saqqa played the full 90 minutes and was instrumental in helping Eskisehirspor keep a clean sheet despite their numerical disadvantage.
Eskisehirspor moved into 11th place with 29 points, five above the drop zone as they allayed their relegation fears.
Al-Saqqa, 35, is hoping to return to Egypt fold, having made his last national team appearance in June 2007 when the Pharaohs met Kuwait in a friendly game.
Egypt coach Hassan Shehata said recently he was considering recalling the veteran defender.
However, the former Genclerbirligi and Konyaspor man was not included in the six-time African champions' squad for Sunday's World Cup qualifier against Zambia.