The 22-year-son of a former national team captain delivered a stellar performance in attack to help provide the perfect start to the tournament for the Gabonese who are co-hosting the 16-team event with neighbours Equatorial Guinea.
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"The pressure was intense but we came through it," said a smiling coach Gernot Rohr. "We played very competitively and it's a really good beginning."
After a quiet start to the game, Aubameyang brought the 40,000 spectators to their feet when he ghosted in at the back post to squeeze home a header and put his team ahead just as they were becoming frustrated by their unfancied opponents.
A diving header from the Saint-Etienne striker on the stroke of half-time set up the second goal. Niger goalkeeper Daouda Kassaly made a brilliant save to stop Aubameyang's effort but the rebound fell perfectly for Stephane Nguema to net from close range.
Aubameyang was also a central figure in the goalless second half, orchestrating a wave of attacks, taking set-pieces and generally keeping Niger on the back foot until he was replaced late on by veteran Daniel Cousin.
Poor defence from Niger contributed to the ease with which Gabon passed the ball around as the Nations Cup new boys looked out of their depth.
Niger threatened rarely and were poorly organised, even after calling in former Olympique Marseille coach Rolland Courbis to help with the preparations.
They also played the last 15 minutes with 10 men when Moutari Amadou was carried off on a stretcher having already made their three substitutions.
