Jose Sosa put Trabzonspor ahead from the spot in the 79th minute, while Nwakaeme added the second seven minutes from time.
The 30-year-old has now scored seven goals in 19 league appearances for his club this season.
Former Super Eagles captain John Mikel Obi also featured for Trabzonspor in the game.
Mikel, who played the entire duration of the game has made 15 league appearances for the club this season.
Trabzonspor moved to top position in the table following the win.
In the Italy, Simy Nwankwo bagged the winning goal for Crotone who edged out Cremonese 1-0 at the Stadio Ezio Scida.
Nwankwo scored the decisive goal three minutes from time.
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