The Black-Whites secured the league title with a 5-0 victory over Levadiakos last time out and the 23-year-old helped his side to end the season impressively against Giannis Petrakis’ men.
Akpom broke the deadlock at the hour mark after benefitting from Dimitris Pelkas’ assist.
Yevhen Shakhovs Sealed the victory moments before the end of the game as PAOK ended the season with 80 points from 30 games.
Akpom featured for the duration of the game in his 20th league appearance for the Black-Whites.
The three-time African champions are in Group B along with Burundi, Guinea and Madagascar.