But Victor Moses, who had been doubtful for the match, will play for Nigeria against Burkina Faso at Soccer City.
Emenike suffered a hamstring injury in Nigeria's 4-1 semi-final win over Mali after he had scored his fourth goal of the tournament giving him the same number as Ghana striker Mubarak Wakaso, who played his last game on Saturday.
Emenike is replaced by Spanish-based striker Ike Uche.
There is again no place in the Nigeria side for captain Joseph Yobo, dropped after the first match.
Burkina Faso have included Jonathan Pitroipa, whose suspension for his red card in the semi-final win over Ghana was rescinded by the Confederation of African Football on Friday.