With both teams already knocked out, pride was the only prize on the table as qualified Gabon and Tunisia faced off in Franceville at the same time. Morocco made a host of changes, including defenders Benatia (suspended) and Michael Basser (injured), from the team beaten by the co-hosts last Friday.
The Atlas Lions' attack was led by Arsenal striker Marouane Chamakh, and attacking midfielder and captain Houssine Kharja, the competition's joint top-scorer with three goals. Keeper Nadir Lamyaghri made way for Mohamed Amsif. Niger's forward line was spearheaded by captain Moussa Maazou, whose dazzling runs caused the Tunisian defence all sorts of trouble last week.
After Younes Belhanda had earned Morocco a belated first win, coach Eric Gerets said his players had given him the response he was hoping for after getting knocked out with defeats to Gabon and Tunisia.
"We are like a boxer in the ring who gets a kick in the head, he's down but he will stand up and fight again. The crisis after the second game [3-2 defeat to the co-hosts] was terrible, but the players stood up and showed the first signs of life tonight, that's what I needed to see," he said. "My players tried to leave this Nations Cup with their heads held high, having said that our campaign was catastrophic."
With 2014 FIFA World Cup™ qualifying starting in June, the Belgian confirmed he would not be walking away from his job.
Rolland Courbis, the team consultant who assumed control of Niger from manager Harouna Doula after their shambolic opening loss to Gabon, said Morocco had deserved to win. Like Gerets a former coach of Marseille, Courbis added: "We didn't attain our objectives so I congratulate those 'experts' who said Niger would finish fourth, we're fourth.
"Our biggest regret was our first defeat to Gabon, that complicated things," he said. "Niger has lots of qualities and limits, but we were in a difficult group, I wouldn't be surprised if one of the two qualified teams goes alll the way."
With all of Gabon glued to events up in Franceville the L'Amitie stadium was nearly empty. Morocco enjoyed near total possession in the early stages without causing Niger keeper Daouda Kassaly too much concern, Kharja and Youssef Hadji both shooting over the bar.
On 34 minutes Dynamo Kiev's Celtic recruit Badr El Kaddouri had Kassaly charging out of his goal with a close-range shot. Niger defender Kofi Dankwae's stuck out a foot to clear the ball to safety.
But the best chance of the first half fell to the always dangerous Maazou, who neatly controlled a high ball into the area, turned and smashed a shot only for the ball to ricochet off the bar with Amsif beaten. Five minutes from the break, Kharja's Cup came to a premature and painful end when the Fiorentina star left the pitch on a stretcher with a knee injury. Adil Hermach came on in the skipper's place.
Niger, 45 minutes away from an historic first Nations Cup point, held a prayer session before the restart. They were looking at grabbing all three points as Karim Lancina's pinpoint free-kick headed for goal on 46 minutes only for Amsif to safely extinguish the danger.
Approaching the hour mark and another well worked move by Morocco saw Younes Belhanda find Mbark Boussoufa in the box, with Kassaly falling at the Russian-based midfielder's feet to smother the ball.
The biggest cheer of the night came in the 65th minute, when Gabon took the lead up in Franceville. Back in Libreville, good work from Kassaly was keeping Morocco at bay until the 89th minute when Chamakh fed Montpellier midfielder Belhanda, whose sliding right-footed shot broke Niger's hearts.