Pyramids were drawn against AS Manima Union from Congo.
The Egyptian will face his Nigerian counterpart Rivers United.
Pyramids advanced to this role after beating Azzam Tanzanian 1-0 after a goalless draw in Tanzania.
Al-Masry won the Ugandan Revenue Authority with the same result in Alexandria, after a goalless draw in Uganda.
The matches of the second round of 32 of the Confederation will be held between November and December, as the first legs will be held between November 26 and 28.
The return matches will be held from the 3rd to the 5th of December.