Nigeria lost 1-0 at home to Guinea-Bissau on Friday in one of the biggest shocks in Africa Cup of Nations qualifying history.
Mama Balde, who plays for French top-tier club Troyes, scored on 30 minutes in Abuja to take the Djurtus (Wild Dogs) to the top of Group A.
Guinea-Bissau, ranked a lowly 113 in the FIFA world rankings, have seven points, Nigeria six, Sierra Leone two and Sao Tome e Principe one, halfway through the six-round mini-league. The top two finishers progress to the finals.
Nigeria, whose line-up included prolific Napoli scorer Victor Osimhen and are 32nd in the FIFA rankings, were firm favourites to win at home and extend their advantage to five points.
But after a bright start, with Osimhen coming close to scoring on 16 minutes, the Super Eagles battled to create clear-cut scoring opportunities in the capital city.
As the match reached the half hour mark, Balde raced on to a lofted pass and fired a low shot past goalkeeper Francis Uzoho.
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Guinea-Bissau nearly doubled their lead soon after, but Euciodalcio 'Dalcio' Gomes hit the side netting with the Nigerian defence in disarray.
Osimhen, who has been linked with a move to Manchester United or Arsenal, became increasingly frustrated as poor service and close marking restricted his threat.
In a Group K shock, Liberia came from two goals behind to draw 2-2 with South Africa in Soweto, where Mohammed Sangare scored an added-time equaliser for the west Africans.
Lyle Foster netted twice for the home team in the first half and Tonia Tisdell halved the deficit entering the final quarter of the match.