Fenerbahce forward Melih Bostan scored, what proved to be the only goal of the game, in the first half as Paul Osam's team were unfortunate to come away with the loss.
Ireland did well to nullify a Turkish team that had beaten Belgium, England and Serbia this season.
The Boys in Green were forced into an early change when James Abankwah collided with Emre Biligin in the Turkey goal while trying to meet a Jamie Mullins cross.
With Abankwah off the pitch, Ireland were temporarily down to 10 men and the hosts almost capitalised when they broke forward but Mahmut Afsar's effort just went wide of the post.
In the 20th minute Turkey took the lead. A free-kick was floated to the front post and Bostan converted the cross to make it make 1-0.
Bostan almost had his second of the game when he unleashed a fine shot that fired back off the post following neat play by the home side.
In the second half Bohemians man Reece Byrne made a fine save to prevent Adem Metin Turk giving Turkey a two-goal cushion.
Ireland continued to press and looked dangerous from crosses by Cian Kelly and set pieces which caused the hosts problems.
They almost got the goal their play deserved when Darragh Reilly put Dara McGuinness through with the goalkeeper but the Turkish stopper got there in time before the forward could capitalise.
Next up for Ireland is Kosovo on Sunday as they look to secure their second win of the group stages.
Republic of Ireland: Byrne, Nevin, Ryan, Reilly (C) (Curtis 81), Aaron O’Reilly, Abankwah (Grehan 12); Mullins (Lonergan 58), Abada (Power 78), Kelly; McGuinness, Agbaje (Nzingo 81)
Turkey: Bilgin, Yilmaz, Tintis, Ortakaya, Cagliyan, Bilgic, Bostan (C), Karademire, Afsar, Guven, Kabasakal
Substitutes: Yilmaz, Tutar, Turk, Akgeyik, Ekelik, Akman, Birinci, Kerem, Ilkhan
Aegean Cup Fixtures
January 19: Ireland v Kosovo, Altinordu Gündüz Teki̇n Onay Sahasi, Turkey, KO 9am (Irish time)
January 21: Playoff Fixture, venue TBC, KO 9am (Irish time) / Final, Altinordu Serpi̇l Hamdi̇ Tüzün Sahasi, Turkey, KO 11.30am (Irish time)
January 15: Ireland 1-0 Tanzania
January 17: Turkey 1-0 Ireland