The Super Eagles won the most points in Kigali thanks to a brace in the first half from the Napoli player on loan.
Nigeria defeated Rwanda 2-0 at Amahoro Stadium in Kigali on Friday, reigniting their hopes of making it to the 2026 World Cup finals.
Victor Osimhen's brace handed the Super Eagles the crucial points as Eric Sekou Chelle started his reign as the head coach with a morale-boosting victory.
Meanwhile, unmarked Osimhen scored the opening goal by firing past Rwandan goalkeeper Fiarce Ntwari in the 11th minute. The Galatasaray forward did well to connect to a free kick delivered by Ademola Lookman to give Nigeria an early lead.
The Super Eagles almost doubled their lead in the 24th minute, but Kaizer Chiefs goalkeeper Ntwari did well to parry away a long-range shot directed to the top corner by Moses Simon.
Rwanda's coach, Adel Amrouche, was forced to make a change in the 37th minute when Samuel Gueulette picked up what looked like a knock, and Gilbert Mugisha was brought on.
Nigeria doubled their lead when Osimhen scored in the third minute of added time of the first half. Samuel Chukwueze picked out Osimhen, who was barely marked again, and the forward with tangible composure fired past Ntwari from just outside the box.
Rwanda could not deal with the Super Eagles attacks, and the visitors took full advantage of the disjointed display by the host.
Nigeria are now placed fourth in the Group C standings - four points behind leaders, South Africa, who defeated Lesotho on Friday in Polokwane.