"Kanu was down with a cold (for the away tie against Equatorial Guinea in Malabo) and that accounted for why he couldn't play any part in the game. He will be back for the return leg in Abuja," said Nigeria coach Shuaibu Amodu.
Chelsea midfielder Mikel Obi, however, remains a doubt for Nigeria after he suffered an injury against Sierra Leone that also ruled him out of the 1-0 defeat of Equatorial Guinea on Saturday. South Africa make up the group.
Nigeria are unbeaten in Group Four of the qualifying tournament for both the 2010 FIFA World Cup and CAF Africa Cup of Nations in Angola, having recorded nine points from three matches.
Victory on Saturday over Equatorial Guinea will guarantee them passage to the CAN finals as well as qualification to the next stage of the FIFA World Cup qualifiers.