Kenneth Omeruo headed into the Guinean net a decisive goal in the 73rd minute, in the Super Eagles second match in Group B of the African Cup of Nations.
The goal, with Moses Simon providing the assist, will catapult Nigeria into the second round of the tournament, if the Guineans were unable to equalise.
Nigeria are heading the group after beating Burundi in the first match.
The Eagles, playing without captain Mikel Obi also dominated possession in the second match at Alexandria Stadium.
The Eagles already lead the group with three points after beating Burundi 1-0, while Guinea are level with Madagascar on one point.