Emmanuel Emenike gave the Super Eagles the lead just before the break and although Cheick Tiote equalised early in the second half, Sunday Mba's deflected effort won the game for Nigeria, who will now face Mali in the last four on Wednesday.
Boubacar Barry, Yaya Toure and Gervinho all returned for the Elephants after they were rested for the 2-2 draw against Algeria. Fedor Ogude was suspended for Nigeria but John Obi Mikel returned, while Super Eagles captain Joseph Yobo was not 100 per cent fit having picked up a knock in the opening match of the competition.
Nigeria created the first chance after just six minutes when a Victor Moses free-kick from the right was headed over the bar by Brown Ideye from six yards out. Souleymane Bamba produced a overhead kick from a Romaric corner after 13 minutes, but his effort went over the bar. Nigeria had the best chance of what was a dull opening 30 minutes when Ideye played the ball through to Emenike on the counter-attack, only for the Spartak Moscow man to screw his shot wide from inside the box.
Emenike made up for that miss three minutes before the break, though, rifling home a 25-yard free-kick past Barry. The goalkeeper would have been disappointed with his effort, flapping at the ball as it whistled past his head and into the net.
Côte d'Ivoire were level three minutes after the interval when Didier Drogba's free-kick from the left was headed home by Tiote from close range. Nigeria fought back and almost took the lead were it not for Barry, who atoned somewhat for his earlier error.
Moses' outswinging corner found Ideye at the far post but his close-range header was blocked by the stopper. His counterpart at the other end, Vincent Enyeama, was next to impress by parrying Yaya Toure's powerful shot from the edge of the area to safety.
Nigeria took full advantage of Enyeama's save when with 12 minutes left Mba ran at the Côte d'Ivoire back-line and, with few options available, he opted to shoot. The ball deflected off Bamba and Barry who could only watch as the ball looped over his head and into the top corner.