Guinea started the better side with striker Sekou Camara glancing Mohamed Bangoura's inviting cross over the Sudan goal after three minutes.
Elsamani turned provider for Sudan’s opener with a curling left footed corner which lanky defender Suliman Omer headed to the top corner of Kanteh's goal.
Guinea continued to push for the equalizer but were denied by Sudan keeper Akram Elhadiwho dived to his left to save Sekou Camara's cracking effort just inside the area.
Mohamed Bashir Ahmed thought he had given Sudan a two-goal lead but his long range curler crash against the wood work five minutes before the break.
Sudan won a penalty on 65 minutes but striker Saifeldin blast it over the goal to ease the pressure on goalkeeper Kanteh after conceding the spot kick.
Minutes later, the El Khartoum forward reacted first to a deflected back-heel pass to find the back of the net via the keeper's legs in late in the game.
Sudan keeper Akram produced a last minute save to deny Ibrahim Sory before defender Deseri Yaovi tapped the rebound wide.
Sudan occupy second place behind host Morocco on goal difference on three points apiece whilst Guinea and Mauritania follow in that with no point.
Logarusic Zdravko Zrvatsko (Head Coach, Sudan)
The game was very interesting and open because both teams got their chances. Even a draw would have been good for either side. What is important for us now is to focus on the next match.
We are taking it game by game because in this group Morocco are the favourites and they can kill you in 15 minutes so we have to fight for the second place and winning today will help us in achieving our target of making the knockout stage.
My team played well and they defended as a team so I am satisfied with our display. When I came to Sudan what I told them is I cannot teach you skill but I can help you in tactics and improve on how to play without the ball.
Mohamed Kanfory Bangoura (Head Coach, Guinea)
The content of our play was not bad but the defending wasn't good in my view, but we have two matches to rectify that. Sudan has experience players who have been together for a while but generally we failed to make our dominance count.
I have no regrets with my choices by playing Mohamed Bangoura at left back as he has been good in the qualifying stage. I will continue with him and I believe he played well despite the loss.
We came here to play three group matches and we respect every opponent so I didn't underestimate Sudan. Our people have to be patient with us we will go back and look at the video and try to address the problems and I hope we will all draw lessons from there.