Trabzonspor now travel to Belarus next week to face Dinamo Minsk in the first round proper.
Derry boss Declan Devine will have been delighted with the blank scoresheet at the break, his 4-5-1 tactics working well. Indeed, it could have been so different had the home side scored with their only clear-cut scoring chance of the opening period.
On the half hour, Patrick McEleney backheeled the ball into the path of Eoghan Osborne and his teasing cross was met by the Ruaidhri Higgins whose header was parried before being gathered by keeper Onur Kivrak.
Trabzonspor’s Olcan Adin also forced Derry’s Ger Doherty into a save following a deft flick with the outside of his foot in the 33rd minute as the Candystripes continued to battle.
After the break Higgins went close again when his header following a Paddy Kavanagh corner was touched over by Kivrak in the 54th minute.
But one minute later, Derry’s dream ended when Trabzonspor broke the deadlock with a very soft goal.
Patrick McEleney played a stray pass when attempting to clear the ball and the alert Brazilian, Paulo Henrique, was on hand to dribble his way through and poke the ball beyond Doherty.
The visitors had a second when speedy right winger, Sen, burst clear and his superb centre was controlled by the advancing Henrique who gave Doherty no chance with a magnificent finish.
With the tie completed, Derry conceded another goal in the 90th minute, through substitute Abdulkadir Ozdemir
DERRY CITY: Doherty; Madden, Greacen, S McEleney, Osborne; Kavanagh (Duffy, 72), Higgins, Molloy, McBride (Houston, 79), P McEleney (McNamee, 63); McDaid.
TRABZONSPOR: Kivrak; Yavru, Kacar (Demir, h/t) , Yumlu, Celuska; Akgun, Colman (Ozdemir, h/t); Sen, Mierzejewski (Aydogdu, 82), Adin; Henrique.
Referee: Michael Lerjeus (Sweden).
Selected other results: St Johnstone 1 Rosenborg 1 (St Johnstone win 2-1 on agg), Hibernian 0 Malmo 7 (Malmo win 9-0 on agg).