The African Nations Cup hosts fell behind to an early Burkina Faso goal but the Dortmund star scored his second of the tournament from the spot. Cameroon beat Guinea-Bissau to take charge of the group.
Gabon 1-1 Burkina Faso (Aubameyang 38' pen, Nakoulma 23')
Pierre-Emerick Aubameyang has done it once more. Having scored in the drawn tournament opener, the Gabon captain came up with the goods for a second time but his side had to again make do with a share of the spoils in Libreville.
Burkina Faso had opened the scoring after 23 minutes when Prejuce Nakoulma scored a superb goal following a quick break. Nakoulma only came on as an 11th minute substitute when the tournament injury curse struck again, this time affecting star man Jonathan Pitroipa.
Aubameyang was forced to dig his side out of a hole, converting the 38th minute spotkick after a foul by Burkina Faso goalkeeper Herve Koffi.
The draw leaves Gabon on just two points from two games and with their knockout stage hopes hanging in the balance. Burkina Faso also have two points.
With Gabon's final group game coming against Cameroon on Sunday, Aubamayeng may have to pull out all the stops again if his nation are to avoid an embarrassing early exit.
Gabon's task has been made harder by Juventus midfieder Mario Lemina being ruled out of the rest of the competition. He did not play on Wednesday because of a back injury and coach Jose Antonio Camacho confirmed his tournament was over.
Cameroon 2-1 Guinea-Bissau (Siani 61', Ngadeu 78', Piqueti 13')
Cameroon took charge of the group after coming from behind to down Guinea-Bissau.
Piqueti gave the underdogs the lead with a right-footed shot inside the area and once mighty Cameroon, who last won this tournament in 2002, looked in big trouble.
Some of the famous names of old are gone and Schalke's Eric Maxim Choupo-Moting decided to skip the Nations Cup, leaving Cameroon as a shadow of the side they used to be.
But they pulled themselves off the canvas with Sébastien Siani scoring from outside the box just after the hour mark and Michael Ngadeu-Ngadjui also scoring from distance to complete the turnaround.
Cameroon now boss the group with one set of matches left to play. They have four points while Guinea-Bissau remain on one.