It was a cagey opening half from both sides, Nigeria dominated most of the possession but failed to make it count with no real chance created.
Nigeria's Super Eagles expectedly started the strongest and had the first effort of the game when a fortuitous bicycle kick from Wilfred Ndidi went wide early on.
In the 10th minute, Tunisia, who was without seven players and their manager due to COVID-19, had the game's only real chance in the opening 45 minutes but Nigeria's defence was alert to clear from the line.
Moments later, Joe Aribo's shot from a Moses Simon corner was expertly blocked by Montassar Talbi.
Another attack from Nigeria in the 16th minute saw Taiwo Awoniyi fail to connect to a lovely outside-the-foot pass from Samuel Chukwueze.
A very cautious start to the second match in the round of 16 ends with nothing to separate the two Eagles at the break.
Two minutes after the restart, Tunisia took a shock lead after an Ola Aina mistake.
Yourself Msakni took advantage, evaded a Nigerian defender before letting fly from outside the box a shot that goalkeeper Maduka Okoye parried into his net to give Tunisia a 1-0 lead.
The Carthage Eagles grew in confidence after that goal and took control of the game at Garoua.
Five minutes after the hour mark, things went from bad to worse for the Super Eagles as substitute Alex Iwobi was sent off for a dangerous foul, six minutes after coming on.
Nigeria quickly put behind them the incident and pile on the pressure in search of the equaliser and almost found one through Moses Simon.
But his left-footed effort was superbly saved by the Tunisian goalkeeper before Umar's late effort went agonising close on the stroke of the 90.
The Carthage Eagles held on for the win to qualify for the last eight where they will face Burkina Faso while Nigeria's Super Eagles will be heading home.