The Nigerians enjoyed an encouraging start to the game, a Aminu Umar struck the upright after eight minutes.
Honduras started seeing a bit more of the ball as the half went on and could have taken the lead after 23 minutes, but Daniel Akpeyi produced a fine save to keep out Rommen Quioto from distance.
Nigeria showed some real attacking intent and were rewarded in the 32nd minute thanks to a strike from Sadiq Umar, with John Obi Mikel picking up the assist.
The Dream Team were in control after taking the lead and managed to deny the Hondurans a clear-cut for the rest of the first half.
Nigeria doubled their lead five minutes into the second half, as Aminu Umar fired home a right-footed effort from inside the box.
Umar completed his brace just before the hour-mark when he latched onto a ball from Mikel, before firing into the bottom corner, 3-0.
Honduras managed to reduce the deficit in the 70th minute when Anthony Lozano clinically slotted past Akpeyi from close range.
The Hondurans pulled another goal back in the 86th minute, as Marcelo Pereira headed home Oscar Salas’s free-kick to set up a nervy finish.
However, the Nigerians managed to see off the late surge to claim the victory and the bronze medal.