In-form Kelechi Iheanacho, Wilfred Ndidi and Victor Osimhen started for the Super Eagles after Alex Iwobi, who tested positive for Covid-19 missed out.
With Sierra Leone and Lesotho playing to a goalless draw in the earlier match of the day in the group, it ensured the Super Eagles progression to the AFCON finals next year.
However, Nigeria still looked to stamp their authority on the clash following the first five minutes but neither one was able to get on the end of Osimhen's delivery and pounce.
Osimhen then opted to take matters in his own hands towards the half-hour mark, but couldn't make use of a golden chance as goalkeeper Saturnin Allagbe gathered the strike.
The host were still on the ropes as the match headed to halftime after Iheanacho dragged a pass from Henry Onyekuru wide of the mark before Allagbe parried a header from Zaidu Sanusi.
Nigeria were on the back-foot seven minutes from the break nearly as Steve Mounie pulled two guilt-edge chances from close-range wide.
Gernot Rohr's side regained control on 56 minutes and saw Osimhen struck the foot of the post with a curling attempt before Sanusi ballooned the rebound.
Nigeria turned to the bench for inspiration inside the last 20 minutes and removed Iheanacho ahead of Paul Onuachu.
The Super Eagles broke the host' hearts in the final minute of when substitute Onuachu netted the winner with a poachers finish to extend his side's lead at the top of Group L.