Vladamir Koman had given Eyup Arin‘s men a sixth minute lead from the spot before Souza brought the tie to level just three minutes later.
In the 22nd minute, Aatif Chahechouhe gave the Yellow Canaries the lead for the first time in the game. And Emenike, a 74th minute substitute for Moussa Sow, rounded off the victory with a goal on the stroke of fulltime.
The 30-year-old last saw the back of the net for his Turkish side in a topflight encounter against Konyaspor in October 2016. And the strike ensures he finished the season with four goals from 16 league outings.
Fenerbahce ended third in the Turkish topflight log after garnering 64 points, 13 behind runaway champions, Besiktas. And will participate in next season’s Uefa Europa League.