Nwakaeme put the visitors ahead in the 28th minute, albeit, the goal was cancelled out by referee Erkan Ozdamar after VAR replays ruled that the Super Eagle had been in an offside position.
Five minutes into the second-half, Anastasios Bakasetas handed Trabzonspor the lead. With goalkeeper Abdulsamed Damlu punching out a dangerous free-kick, the Greek forward picked the rebound, controlled the ball before unleashing a beauty past Damlu.
That strike saw the hosts come out in their numbers in search of an equaliser. However, their efforts met strong resistance from a solid Black Sea Storm backline.
In the closing stages of the tie, Nwakaeme had the final say – dribbling past Issam Chebake before sending a ferocious shot past the goalkeeper.