كتب : وكالات
Abdul-Hamid Bassiouny scored twice for Al-Hodoud but the home side equalized through two spot-kicks before snatching the winner deep into the injury time.
The first leg in Alexandria two weeks ago ended in a goalless draw.
The Egyptian side finished the game with nine players after Mohamed Halim and Ahmed Kamal received their marching orders three minutes from time.
Al-Hodoud is the third Egyptian side to exit African competitions after city rivals Ittihad were eliminated from the same tournament while Enppi bowed out of the African Champions League.
African champions Ahli are the only Egyptian side remaining in the African Champions League this season.