كتب : Hatem Maher
Guinea went two up, thanks to two strikes from skipper Pascal Feindouno and Ismael Bangoura either side of the interval.
Substitute Hicham Aboucherouane narrowed the deficit few moments after Bangoura's strike but a Feindouno spot kick dashed Morocco hopes.
Feindouno was then red-carded for lashing out at Amine Rbati in an off-ball incident.
Abdeslam Ouaddou's header in stoppage time wasn't enough for Morocco to snatch a precious equalizer.
Morocco are temporarily in charge of Group A with three points, on level with hosts Ghana and Guinea.
The Atlas Lions have an uphill to climb if they are to reach the quarter-finals as they face Ghana in the last group stage match, while Guinea have an easy task against outsiders Namibia.
Morocco keeper Khalid Fouhami gifted Guinea the opener after 11 minutes.
The Raja Casablanca guardian prepared himself to handle a cross from Feindouno's free-kick but the Saint Etienne man deceived him after firing straight into the net.
Morocco's display was nowhere near the one they produced in the 5-1 drubbing of Namibia.
They failed to threat the Guineans in a dull first-half, making only a tamed shot from Youssef Hadji in the 24th minute.
Fouhami was on alert in the 36th minute when he tipped Fode Mansare's free-kick from underside the crossbar.
Morocco's first real threat came three minutes after restart when Hadji's superb shot with the outside of his right foot was blocked by Guinea keeper Kemoko Camara.
The match afterwards was a much livelier affair.
Bangoura extended Guinea's lead in the 59th minute after capitalizing on a dreadful marking by Badr El Kaddouri.
He escaped the Dinamo Kiev defender to control Feindouno's through pass inside the area and coolly slot past Fouhami.
Aboucherouane, who replaced Houssine Kharja in the second-half, narrowed the gap just one minute later with a splendid shot.
He cracked a left-footed shot from the edge of the area that went into the top corner of the net.
However, Morocco's hopes of snatching an equalizer were dealt a major blow when Souleymane Youla was awarded a penalty three minutes past the hour mark.
Youla got the better of Michael Chretien, who had no alternative but to bring him down to prevent him from going clear on goal.
Feindouno stepped up and successfully converted the penalty despite Fouhami's desperate attempt to block it.
However, he had to leave the pitch in the 67th minute after striking Rbati's foot with his boot, just in front of the referee who spotted the incident.
Ouaddou notched a consolation in the additional time with a free header from inside the area.