The Pharaohs needed extra-time to see off the Cheetahs at Stade Adrar on Monday after Jodel Dossou (83') cancelled out a 69th minute opener from Marwan Attia.
Yasser Ibrahim fired home after 97 minutes, and Mohamed Salah sealed the result with his goal on 124 minutes.
Egypt will now play AFCON holders Ivory Coast, who defeated Burkina Faso 3-0 in their first knockou match.
Reflecting on the game, Hassan explained that there are no easy games at AFCON.
He told CAFOnline: "It was a very difficult match. Before the game, I said there are no easy teams, and Benin were a tough opponent.
"We work to analyse every opponent in order to adapt our game. Egypt is a great football team and I want to make my people happy.
“I trust my team and my staff, especially the medical staff, to ensure good recovery before the next match.”
Mostafa "Zico" Mohamed has credited Egypt coach Hossam Hassan for helping unlock his confidence after continuing his impressive rise with another influential display at the 2026 FIFA World Cup.
Mohamed Salah inspired Egypt to a historic 3-1 comeback victory over New Zealand in Vancouver, helping the Pharaohs claim their first-ever FIFA World Cup win and move to the top of Group G.
Romelu Lukaku made another decisive statement from the bench as Belgium were held to a 1-1 draw by Egypt in their 2026 FIFA World Cup Group G clash, with coach Rudi Garcia insisting the striker will not be rushed back into the starting XI.
Egypt head coach Hossam Hassan has insisted his side are "not here to make up the numbers" after they were held to a 1-1 draw by Belgium in their opening 2026 FIFA World Cup Group G match.
