Collecting a pass from Mustafa Eskihellac, the former Scotland youth international drilled the ball past goalkeeper Cenk Gonen from close range.
That lead lasted for 15 minutes as the hosts equalised through Hugo Rodallega, after the Colombian forward curled a beautiful past goalkeeper Ertac Ozbir from the edge of Malatyaspor’s goal area.
A minute before the half-time break, they took the lead courtesy of Turkish midfielder Recep Niyaz, who controlled a pass from Muris Mesanovic before slotting the ball past onrushing Gonen.
In the 77th minute, Benjamin Tetteh brought YMS to level terms with a simple tap-in after goalkeeper Ozbir had fumbled a header from Adem Buyuk.
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.