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.
Regardless of that match, qualification for the quarter-finals will now be decided in the last round of group games on Sunday.
"The Ivory Coast won the last Africa Cup of Nations after drawing their opening two games," recalled Gabon coach Jose Antonio Camacho.
"Maybe it is a good omen. Everything still depends on us. If we beat Cameroon we will qualify."
Gabon had been dealt a blow ahead of the match with the loss of Juventus midfielder Mario Lemina to an injury that Camacho confirmed will rule him out of the rest of the tournament.
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 -- Camacho also confirmed he will not feature again at the tournament -- but they 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.