Goals from Lalaina Nomenjanahary and Charles Andriamatsinoro in Alexandria earned the Indian Ocean islanders a famous victory and saw Madagascar pip three-time winners Nigeria to top spot in Group B.
"I have to thank the players who made me proud and the people of Madagascar proud. It's a real achievement for us," said Frenchman Dupuis, who combines his role with a job at a lower-league club in his homeland.
"When I saw the group we were given we all put Nigeria as favourites. Nigeria are still a strong favourite for the tournament."
Madagascar will face one of four best third-place finishers in the last 16 after becoming the first newcomers since Cape Verde in 2013 to survive the group stage.
"I find that the players are more and more concentrated," said Dupuis. "But I have always played the same players and that's going to be a major problem now.
"We're going to have 10 of them resting at training. The main problem is that Marco (Ilaimaharitra) received a second yellow card and won't be able to play in the next match."
He added: "I really wanted to make the Madagascar people dream and we did but it came at a bit of a cost with all the effort we put in."
Nigeria counterpart Gernot Rohr said he believed Madagascar were capable of creating further surprises, remarkable for a team that needed to come through a preliminary round just to reach the qualifying competition.
"You (Madagascar) can go very far now. You beat us, you beat Burundi, a team that's not easy to beat. Anything can happen in knockout games. I think you're capable of doing this again."