Nigerian full back Ola Aina (L) tries to beat Sierra Leonean defender Kakay Osman during the 2023 AFCON qualifiiers between Nigeria and Sierra Leone at Moshood Abiola Stadium in Abuja, on June 9, 2022. AFP
Jonathan Morsay stunned the hosts with an early goal after 11 minutes, but Alex Iwobi leveled the score four minutes later.
Forward Victor Osimhen scored the winner for the Super Eagles four minutes before the break.
Nigeria are leading group A with three points on level with Guinea Bissau, who hammered Sao Tome and Principe 5-1 earlier on Thursday.
In Group C, Cameroon defeated Burundi 1-0 away from home thanks to Olympique Lyon striker Karl Toko Ekambi, who scored the winner in the 30th minute.
Later in the day, Liverpool midfielder Naby Keita scored a last-gasp winner, helping Guinea defeat Malawi at home in a Group G match.
Guinea lost 1-0 to Egypt in the Group opener on Sunday.
In Group H, Ivory Coast drew 0-0 with hosts Lesotho to keep their place at the top of the group with four points.
The winners and runners-up of the 12 groups will reach next year's Africa Cup of Nations in Cote d'Ivoire.
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