The Eagles of Carthage advanced to the quarter-finals thanks to a long-range effort from Tunisian playmaker Youssef Msakni in the 47th minute.
Nigeria, the only side to win all three of its group stage games, might have staged a comeback if Alex Iwobi's red card in the 66th minute had not been shown.
Tunisia, who had fallen twice in the group round and qualified as one of the best third-place teams, shut out Nigeria in a tense game in Garoua on the first day of the knockout play.
Nigeria's Joe Aribo said, "We allowed them to acquire a footing in the game." "It's impossible to take anything away from them, but we should have done a better job."
Tunisia won despite the absence of coach Mondher Kebaier, who opted to stay in his hotel room rather than stand on the sidelines after testing positive for the coronavirus.
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