Mali, who came third in last year’s tournament, scored six minutes from time through ex-Barcelona star Keita, who capitalised on an error from Niger goalkeeper Daouda Kassaly in Port Elizabeth.
Cheick Tidiane Diabate had a chance for Mali four minutes in, but his drilled shot across the ground provided an easy save for Mena goalkeeper Daouda.
Mali’s Cheick Fantamady Diarra almost broke the deadlock on 15 minutes – hitting the ball way over the Niger goal from 12 yards out after Mahamane Traore’s dangerous cross.
Traore nearly scored himself a minute later with a powerful volley from distance, but the OGC Nice midfielder sent the ball sailing harmlessly wide of the post.
Niger should have pulled ahead 21 minutes in when Molla Wague’s tight-angled shot from inside the Mali box smashed into goalkeeper Mahamadou Samassa.
Cheick Diarra missed a decent opportunity for the Eagles on the half hour mark – failing to connect with Keita’s free-kick, deep inside the Niger penalty area.
The Rennes midfielder missed another chance six minutes before the break, sending a potent free-kick well over the crossbar from 30-yards out to round of a largely disappointing half.
Mohamed Soumaila drew the game’s first yellow-card three minutes after the break for a rash challenge on Traore.
Mali captain Keita came close nine minutes after the break – the 33-year-old forcing an impressive save from Niger goalkeeper Daouda Kassaly.
Samassa could only find the side-netting for the Eagles on 65 minutes, after making some decent space for himself deep inside the Niger penalty area.
Niger – who have never won a tournament point – almost snuck ahead nine minutes later, but Moussa Maazou’s header sailed over the Eagles’ bar following a Mena corner.
Keita came close 13 minutes from time – the former Barcelona star ratting the Niger crossbar from the edge of the box.
But he made no mistake in the 84th minute, his predatory instincts and finishing power on full display after Kassaly’s punch clear from Fousseiny Diawara’s cross landed neatly at his feet.
Mali face four-time champions Ghana on Thursday and will have a great oppurtunity of sealing the top spot in Group B.