PSV's goals at Istanbul Basaksehir Fatih Terim Stadium came from English midfielder Noni Madueke in the 37th minute and Dutch midfielder Marco van Ginkel in the 59th minute.
Galatasaray's only goal was scored by Senegalese forward Mbaye Diagne in the 84th minute.
The Istanbul club lost the first leg match 5-1 at PSV Stadium on July 21.
Turkish club will face Scottish team St. Johnstone in the UEFA Europa League third qualifying round after this result.
