Al-Farouq Aminu, Michael Umeh and Michael Gbinije combined for 43 Nigeria points as Will Voigt's men were in control for much of the contest.
A day after performing one of the biggest upsets in the tournament so far by eliminating Cape Verde, Gabon seemed powerless to oppose Nigeria's determination in reaching the last four of the tournament.
They will continue their campaign in the Classification Games.
Nigeria return to the Semi-Finals for the first time since 2011.
The Western Africans will face the winner of the Quarter-Final between Senegal and Algeria.
As a result of the win, Nigeria secured a place in the Olympic Qualifying Tournament, an event destined for teams that finish in the top-4 of the African Championship.
Turning Point: Nigeria closed the first quarter with a 12-point lead and Gabon never posed a threat.
Stats Don't Lie: Nigeria's excellent ball movement - which resulted in 23 assists - was in stark contrast to Gabon's modest attack plan and that made all the difference. The Nigerians led by as many as 41 points.
Game Hero: Just as he did in the Round of 16, Mayimba came off the bench to lead Gabon with a team-high 21 points.
The Bottom Line: Nigeria's dream of winning a first-ever African title remains alive as they displayed clear superiority at all aspects of the game. Gabon never gave up and know they will return home with at least one victory.