Hodoud scored a three-minute double salvo through Ahmed Eid and Ahmed Abdul-Ghani in the 14th and 17th minute before Kouassi Blaise pulled a goal back for the visitors in the 21st minute.
Abdul-Hamid Bassiouni restored the Egyptians' two-goal lead six minutes before the interval.
In the second half Sfaxien pilled in the pressure and Mohamed Qadouri missed a golden opportunity to bring his team back in the game on 69th minute but William Mensah brilliantly turned his effort to corner.
Organized Hodoud's defense showed a lot resilience and Amr Al-Dali could have extended their lead in the 89th minute but he blazed a rebound over the bar from Jassem Khallufi's save.
The win lifts Hodoud top of group A in the Confederation Cup quarter final with six points, two points ahead of second place Sfaxien.