A 73rd-minute header from Kenneth Omeruo gave Nigeria all three points against their fellow West Africans.
This means Nigeria have sealed a place in the round of 16 having grabbed six points from two matches.
Speaking after the game with the Nigerians, Put rued the loss, saying his boys put out a great showing on Wednesday.
“It was lack of concentration at that moment and they got the goal and that was very hard because I think the players came out and actually perform well,” he told Brila FM.
“They did everything possible but we just didn’t have the luck on our side.”
Guinea are now in a tight corner in Group B as they have only one point from two games which leaves them with no option than to win their last match with Burundi to make it to the next stage.