It was a goalless first half, in which the Walya Antelopes gave a good account of themselves, and even had a goal disallowed after Godfrey Oboabona made a goalline clearance in the 23rd minute.
Behailu Assefa gave the hosts a shock lead in the 56h minute, after Vincent Enyeama mistimed his cross, which was adjudged to have crossed the line before the Super Eagles stand-in captain got hold of it.
The noisy fans at Addis Ababa Stadium were however silenced when Emenike produced a goal out of nothing to equalise for Nigeria with a terrific shot from outside the box.
The goal appeared to imbue the African champions with more confidence, as they played a more composed game, with Ahmed Musa striking a shot against the upright after tricking his way into the Ethiopia box.
The Ethiopians, however, had their moments, as Oboabona made a last ditch clearance to deny Saladin Said a clear chance at goal.
Emenike scored from the penalty spot in the 90th minute to seal the win for Nigeria after he was brought down inside the box by an Ethiopian player.
Nigeria now have one leg in Brazil, as they hold the advantage going into the second leg of the play-off which is scheduled for November 16 at the UJ Esuene Stadium in Calabar.
Nigeria line-up: Enyeama, Efe, Elderson, Oboabona, Egwuekwe; Onazi, Mikel, Oduamadi; Moses, Musa, Emenike