The Eagles came third last year but looked to be heading for a goalless draw until ex-Barcelona midfielder Seydou Keita struck six minutes from time.
And the 42-year-old one-time Sunderland defender – one of only a handful of managers to remain from last year’s competition – admitted his opponents were hard to break down.
“It was a difficult game against a very defensive team like Niger,” said the Frenchman.
“But I’m happy for the players because they have worked hard and this win will boost confidence for the next match against Ghana.”
The result takes Mali to the summit of Group B after Ghana and Congo drew 2-2 earlier today.
The Eagles face the four-time champions on Thursday with a win all but sealing their progression to the quarter-finals.
Niger boss Gernot Rohr – who once managed Bordeaux in a Uefa Cup final – was pleased with the effort his players showed despite the result.
Mena came within six minutes of winning their first-ever tournament point – the West African side appearing for only the second time.
And 59-year-old Rohr, who has previously coached fellow African side Gabon, admitted he could not ask more from his players.
“We tried our best against a top team like Mali,” said the German.
“My players have great fighting spirit and big hearts, so you can be happy even when they lose.”
Niger face Congo on Thursday needing a win to climb off the foot of the group.
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