A 90th-minute penalty following a moment of defensive folly handed Nigeria an away win in Addis Ababa and set them up for a routine assignment in the return leg in Calabar on November 16.
Emenike had been tugged by defender Aynalem Hailu as he got goal side in the last minute in a clear infringement and got up to convert the resulting spot kick with ease.
Before that, he had struck a snap shot in the 67th minute from outside the penalty area to equalise after the home side had gone ahead in the 56th minute courtesy of a bizarre decision from the linesman.
A miscued cross from left winger Behailu Asefa swerved towards the Nigeria goal and caught goalkeeper Vincent Enyeama unawares, forcing him to catch it perilously close to the goal line.
Cameroon lineman Yanoussa Moussa, whose view would have been obstructed by Enyeama's back, immediately signalled for a goal to the bemusement of the visitors but delight of the home crowd.
It made up for a similar close call in the first half when Saladin Seid had his effort hooked off the line by Nigeria centre back Godfrey Oboabona when the ball seemed to have crossed the line.
Television replays proved inconclusive and without goal-line technology officials allowed play to continue.
Seid proved a thorn in the side of the Nigerian defence but scuffed several good efforts and a draw would have been a fair reflection of a game in which Nigeria also struck the upright when Ahmed Musa saw his 77th-minute shot cannon back into play.
Having snatched the win, though, Nigeria are now overwhelming favourites to qualify for a fifth World Cup, ending a fairytale run over the last 18 months for Ethiopia.
In other African World Cup playoff first legs, Burkina Faso beat Algeria 3-2 and Ivory Coast beat Senegal 3-1 on Saturday. Later on Sunday, Tunisia host Cameroon.