Ahmed Atef’s hat-trick powered the Egyptians past Finidi George’s men at the 30 June Stadium in Cairo on Saturday night.
The Nigerian side held firm in a balanced first half, but their resistance washed-out after the break as the reigning African champions took control.
Atef opening the scoring seven minutes into the second half before doubling the lead five minutes later.
The forward completed his hat-trick 18 minutes from time, sealing a dominant Group A victory for the Egyptians.
In the other Group A fixture, Morocco’s RS Berkane also recorded a 3-0 win over Zambia’s Power Dynamos.
Rivers United will look to respond when they host Berkane next Friday at the Godswill Akpabio International Stadium in Uyo, while Power Dynamos entertain Pyramids FC in Lusaka on the same day.