The Super Eagles went into their final group-stage match knowing a point would secure their progression through to the last-16, though even defeat might still have left them qualifying as one of the best third-placed teams.
It was a relatively sluggish start from Nigeria, but they took a narrow lead into the break. Moses Simon played the ball across the face of goal and, with Victor Osimhen lurking at the back post waiting for a tap-in, Opa Sangante smashed it into his own net.
In an open second-half, Osimhen went close on a number of occasions to getting himself on the scoresheet, having one goal ruled out for handball after he scored from a yard out, and then heading wide when free six-yards out.
Franculino had the ball in the net for Guinea-Bissau, as they pushed for a late equaliser, but he was denied by the offside flag, as was Nigeria's Zaidu Sanusi when he then thought he had scored seconds later.
Nigeria did not find a second goal but it mattered not, as they saw out the match to secure a victory that sees them safely through. The Super Eagles finished second in Group A, behind Equatorial Guinea, and will face Senegal, Guinea or Cameroon in the last-16.
Guinea-Bissau, meanwhile, were left to reflect on an admirable display but ultimately a third straight defeat, as their wait for a first ever win at AFCON goes on.