"I have to thank the players who made me proud and the people of Madagascar proud,” said Dupuis.
“It's a real achievement for us. When I saw the group we were given we all put Nigeria as favourites. I think that Nigeria are still a strong favourite for the tournament."
As a reward for their exploits Madagascar, the first newcomers since Cape Verde in 2013 to reach the knockout stages, will face one of the four best third-place finishers in the last 16.
"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.”
Madagascar will be without midfielder Marco Ilaimaharitra who received a yellow card for the second time in the tournament and will be suspended for the last 16 match.
Dupuis 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."
Gernot Rohr, the Nigeria coach, said he believed Madagascar were capable of creating further surprises.
"Madagascar can go very far. They beat us. They beat Burundi, a team that's not easy to beat. Anything can happen in knockout games. I think they’re capable of doing this again."