The Egyptian outfit were initially announced as winners for the second-round tie after the Senegalese side refused to take the field due to a change in venue on short notice. However, the African football governing body ordered a replay for the second leg.
Milutin Sredojevic's started with an all-out attacking formation, which comprised of Mostafa Mohamed and Youssef Obama while Abdallah Gomaa returned from suspension.
The White Knights showcased their intentions early as the 19th minute when Mostafa Mohamed finished off a well laid delivery from inside the danger area.
Generation began launching into gear following the earlier set back, but the Egyptians maintained momentum to keep their front cushion.
Zamalek made a strong start in the second half; however the visiting side handled the pressure to maintain the balance in the game.
Advantage remained with the Egyptians, who slowly but structurally pushed towards a second of the evening however the Senegalese side held solid ground.
Sredojevic looked to bench in the final 20 minutes and brought on Mohamed Sobhi for Mohamed Awad. However, the Egyptians marched to victory in the end to keep their pursuit of a sixth continental title alive after progressing to the group stages.
Zamalek will now join Group A and will come up against the likes of Primeiro de Agosto, TP Mazembe and ZESCO United.