The move is seen as part of Ukraine's efforts to reinforce its army as soldiers struggle to hold positions against Russia
Prejuce Nakoulma silenced the Stade de l'Amitie as he gave Burkina Faso an early lead but Aubameyang soon levelled from the penalty spot after he had been fouled inside the area.
Gabon had chances to win the game late on but this was the third 1-1 draw in as many matches in Group A, with Cameroon and Guinea-Bissau meeting at the same venue later on Wednesday.
Regardless of what happens in that match, qualification for the quarter-finals will now be decided in the last round of group games on Sunday.
Gabon had been dealt a blow ahead of the match with the loss of Juventus midfielder Mario Lemina to an injury that could rule him out of the rest of the tournament even if the Panthers were to go all the way.
Burkina Faso lost one of their key men, Jonathan Pitroipa, to injury early on but it was his replacement Nakoulma who grabbed the opening goal midway through the first half.
The Kayserispor player latched onto a long punt downfield and held off both Johann Obiang and Merlin Tandjigora as he charged into the box before poking the ball past Didier Ovono in goal.
Obiang then went off hurt for Gabon but Jose Antonio Camacho's side were back on level terms seven minutes before the interval.
Goalkeeper Herve Koffi came charging off his line and took out Aubameyang. The Borussia Dortmund star appeared to have pushed the ball too far in front of him but the Gambian referee had no choice but to point to the spot.
Aubameyang coolly converted the penalty for his second goal of the tournament after his effort against Guinea-Bissau at the weekend.
The match was drifting towards the draw in the second half before Gabon rallied towards the end.
However, when Denis Bouanga met Aubameyang's knockdown with a first-time effort eight yards from goal, Koffi made a superb block with his foot to divert the ball behind.
Substitute Serge Angoue then headed wide from Bouanga's cross as the game ended level.
The move is seen as part of Ukraine's efforts to reinforce its army as soldiers struggle to hold positions against Russia
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