Both sides came out of their opening encounters with the same scoreline, with Gabon denied late on by Guinea-Bissau, while Wednesday’s opponents were held by Cameroon.
Burkina Faso opened the scoring in the 23rd minute through substitute Prejuce Nakoulma, as Gabon’s promising start failed to pay dividends in front of a raucous home crowd in Libreville.
But the noise levels rose again before the interval when talisman Aubameyang netted a penalty after being fouled by goalkeeper Kouakou Koffi in attempting to gather a throughball.
Stallions coach Paulo Duarte’s hopes of securing a win over his former employers were not aided by injuries to Jonathan Pitroipa, Jonathan Zongo and Yacouba Coulibaly, and the fate of both teams now rests on the final round of matches.
Aubameyang had an early sight of goal, but blasted a 25-yard free-kick well over Koffi’s crossbar.
It was the bar that came to Koffi’s rescue soon after as Denis Bouanga’s powerful drive struck the underside of the woodwork, before Aubameyang tamely directed the rebound straight at the goalkeeper.
Burkina Faso suffered an injury blow inside the opening 10 minutes, with Pitroipa appearing in considerable pain as he was taken off the field on a stretcher.
But it was his replacement who broke the deadlock against the run of play, Nakoulma collecting Patrick Malo’s long clearance and bundling through two challenges to find the net as much through good fortune as his own endeavour.
The lead lasted only 15 minutes, with Koffi bringing down the onrushing Aubameyang to concede a penalty which the prolific Borussia Dortmund forward confidently converted to ensure parity at the interval.