The home side took the lead but two goals from the Fenerbahce striker spared the Super Eagles' blushes
The visitors headed into the game as strong favourites for the clash against an Ethiopia side looking to reach the World Cup finals for the first time in their history.
However, the Africa Cup of Nations holders struggled for much of the encounter and fell behind when midfielder Behailu Assefa put Ethiopia ahead early in the second half.
Sewnet Bishaw's men could not hold on to their lead, though, with Emenike levelling with a fine individual goal before completing the turnaround with a late penalty.
Nigeria made the better start to proceedings, with winger Victor Moses and striker Nnamdi Oduamadi both wasting chances to give the visitors the advantage.
Ethiopia were denied a shock lead in the 23rd minute when Saladin Said saw his effort prevented from finding the net by Godfrey Oboabona's goal-line clearance.
Referee Neant Alioum adjudged that the ball had not crossed the line, and Ethiopia were almost made to pay for that missed opportunity when attacker Ahmed Musa forced a fine save from home goalkeeper Jemal Tassew.
Bishaw's side again came close when Nigeria keeper Vincent Enyeama produced a great stop to keep out another Saladin strike just before the break.
But Ethiopia were rewarded for their persistence 11 minutes into the second half, Assefa netting in bizarre fashion as Enyeama caught his deep left-wing cross after the ball had the crossed the line.
But their lead lasted just 10 minutes. Emenike levelled matters with a spectacular finish from 25 yards that left Tassew with no chance.
Stephen Keshi's side gained confidence from that goal, but their hopes of taking victory looked to be fading when Musa struck the post 14 minutes from time.
There was to be a sting in the tail for the hosts though, as Emenike secured triumph with a confident spot-kick in the 90th minute after he had been pulled down by Aynalem Hailu.
The sides will meet for the decider in Calabar on November 16.