The match, which took place at the Tumba stadium in Thessaloniki, ended with Krasnodar's victory with a score of 2: 1.
The goal of PAOK was hit by the home player Yannis Mihailidis, who sent the ball into his own goal, as well as Remi Cabella.
The only goal of the Greek team on account of Omar El-Kadduri.
Krasnodar beat PAOK 4-2 on aggregate and will continue to play in the Champions League at the group stage.
Earlier the line-ups of PAOK and Krasnodar for the Champions League qualification match were announced.