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Keita came close to breaking the deadlock 10 minutes after the restart, only for Niger goalkeeper Kassaly Daouda to deny the captain.
Niger rarely threatened, but they nearly nicked the three points in the final 15 minutes when Maazou headed over from a corner.
Mali came close to snatching a winner with 10 minutes left to play as Keita's strike crashed against the crossbar.
However, the midfielder finally made the breakthrough in the 85th minute when he took advantage of a fumble by Douada to fire in.