Gernot Rohr's side lost all three games on its tournament debut last season and went down to Mali in its opener this year, but it more than held its own against Congo DR, which was a clear favourite coming into the match.
It could have taken all three points but failed to take advantage of a three-on-two situation in injury-time.
The result leaves Congo DR third and Niger fourth, with qualification now down to the final matches against Mali and Ghana respectively.
Niger almost took the lead in the fourth minute when Modibo Sidibe pounced on careless defending and found himself unmarked on the left of the area.
Robert Kidiaba spread himself but Sidibe's attempt to pass the ball across the goalkeeper and into the bottom left-hand corner resulted in the ball coming back off the post.
Congo DR responded with Lomano LuaLua mis-hitting a shot wide when well placed.
It came close to going ahead in the 13th minute when Mulota Kabangu's cross found Tresor Mputu as Niger pushed up.
He controlled the ball with a mixture of chest and head before unleashing a firm, low shot which Kassaly Daouda did well to tip round the post.
Youssouf Mulumbu spurned a great chance in the 35th minute when LuaLua's blocked shot broke for him unmarked in the area, but he fired wide despite having plenty of time and space.
Striker Dieumerci Mbokani thought he had put Congo DR ahead four minutes before the break when he was clean through but Daouda pulled off a great save.
Moussa Maazou's sharp shot was uncertainly parried by Kidiaba after the re-start and the Tunisia-based striker then forced the keeper into a diving save from a header despite being outnumbered by Congo DR defenders.
The game was evenly balanced but there were few clear-cut openings in the second half.
Niger almost scored in the fourth minute of injury-time when it found itself in a three-on-two situation.
Alhassane Dante's 20-yard shot was parried by the keeper, who then intercepted Maazou's lofted cross and the final opening was gone.