Eric Chelle’s side had built a commanding lead through goals from Victor Osimhen, Wilfred Ndidi, and Ademola Lookman at the Fez Stadium before the Carthage Eagles staged a late fightback.
Montassar Talbi pulled one back in the 74th minute, heading in a free-kick from Hannibal Mejbri, and Ali El Abdi converted a penalty in the 87th minute following a handball by Bright Osayi-Samuel.
The Super Eagles faced a nervy finish but held on to claim all three points and secure qualification to the Round of 16 with a game to spare.
Despite receiving criticism for allowing two late goals, the Chippa United captain defended his performance stating that conceding is a natural part of football.
"In a tournament like this, you are bound to concede goals. Even the best teams in the world concede goals," Nwabali told the media.
"I don’t think there is any problem in the defence, I only feel like we need to keep going. I played my first game at last AFCON and we tried to keep a clean sheet in the second game.
"But you know, football has improved a lot. It's not something you just go home, just come out and play. Everyone wants to (win).
"So, we really don't wish to concede, we really wish to keep a clean sheet. It pains me a lot when I concede, but we keep going as a team.
"Also, set pieces are something you can’t correct. We scored through set pieces and they did the same. We won but you can’t correct certain things."
"I was injured, but with the help of the team doctors and the physios, I was able to stand and continue to play," he continued.
"It's quite tough for me, because it's not something you come out to say. But most times, whatever things you see online but I'm always a strong man, so I try to just defend my country. You understand me."
Thanks to the win, Nigeria have secured a place in the Africa Cup of Nations Round of 16 as Group C leaders, regardless of the result in their final group match against Uganda.
Nwabali praised the performance of his teammates, as well as his goalkeeping colleagues Francis Uzoho and Amas Obasogie.
"I'm really proud of these guys, I'm really proud of these players, they try giving everything," he added.
"And winning (Tunisia) and also qualifying is a big boost for us going to the Round of 16. It's a really big boost for us.
"(Uzoho and Obasogie) are nice guys. My first AFCON was with Francis (Uzoho), he is one guy I always wish to work with. I’m not talking about Amas (Obasogie) because I know him in the league (NPFL) before leaving Nigeria but these guys are amazing guys.
"They are like my family, they are like my brothers, and they are everything. They come to me with no bad thoughts, no bad energy."
Nigeria will face Uganda in their final Group C match, aiming to secure a third consecutive win in the tournament.
