Playing at the Ulker Stadium Sukru Saracoglu Sport Complex in Istanbul, Fenerbahce defeated the Ukrainian club thanks to goals from Miroslav Stoch in the 59th minute and Simon Kjaer in the 67th minute.
Zorya Luhansk's Eduard Sobol was given a red card in the 92nd minute.
Fenerbahce are now in first place of Group A with 10 points in five matches. Dutch team Feyenoord are second with 7 points. Manchester United find themselves in third place with 6 points.