Sunday Mba's mazy run set up a dramatic winner 12 minutes from time, sending the Ivorians home empty-handed yet again after another in which they failed to deliver.
Mba, based in the obscurity of the Nigerian league, was allowed to weave his way close to the edge of the Ivorian penalty area before hitting a shot that deflected off former Leicester City defender Sol Bamba and looped over goalkeeper Boubacar Barry.
The goal ensured the match would not go into extra time which both teams looked to have settled for.
Emmanuel Emenike gave Nigeria a deserved half-time lead with a rasping free-kick which Barry tried to punch but completely missed.
The goal came two minutes from half-time and broke the deadlock in a game that offered few chances early on.
The Ivorians left the field bickering among themselves, the referee and their opponents, but were suddenly a much more committed force in the second half, moving immediately into attack.
It took just five minutes for Cheick Tiote to equalise, heading home unmarked at the back post from Didier Drogba's free-kick.
Then followed more dominance from the Ivorians with a blistering shot from Yaya Toure forcing a save out of Nigeria's Vincent Enyeama in the 67th minute.
But Drogba, Gervinho and Toure proved largely ineffective against a Nigerian side whose coach Stephen Keshi had previously warned were far from the finished product.
"We had a 20 percent chance but my boys showed character and this is the character I know that Nigeria have," Keshi told reporters.
Defeat effectively ended the chances of Drogba and other senior Ivorian players winning Africa's top club prize to add to their achievements on the world stage at club level.
Nigeria will play Mali in Wednesday's semi-final in Durban.
