A lone goal by Mama Samba Balde in the 29mins of first half proved to be the decisive moment of the game despite Nigeria’s best efforts to salvage at least a point.
The Nigerian side started the game on a bright note with Villarreal winger Samuel Chukwueze trying to run down the Guinean from the right side.
Napoli forward Victor Osimhen almost put Nigeria ahead midway into the first half but he was caught off on two occasions.
Mama Balde broke the deadlock for the away side in the half hour mark after he received a long pass from the team’s skipper and two Nigeria defenders were caught flat-footed.
The Nigeria coach Jose Peseiro made changes early in the second half, Moses Simon and Paul Onuachu came in for Ademola Lookman and Kelechi Iheanacho.
The Nigeria attack came alive and the biggest chance of the game fell to Simon and Ndidi but both players failed to convert as Guinea went away with a valuable 3 points.
The Djurtus of Guinea Bissau now seat top of Group A with 7points and could brighten their chances of qualification in the second leg billed for Monday in Bissau.
Speaking after the game, Nigerian coach, Peseiro congratulated their opponent, saying they were lucky to run away with the victory, and assured Nigerians that the Eagles would come out stronger in the return leg.
“I want to congratulate the Guinea Bissau for today’s victory. Luck was on their side today. We created many many chances, dominated the game but luck was not on our side” he said.
Defeat meant the Eagles slipped to second place while the Djurtus climbed top, with seven points to the Eagles’ six, ahead of the two teams’ confrontation in Bissau on Monday evening.