The encounter was marred by a number of injuries to both outfits who appeared to struggle to adjust to the pitch in Libreville.
It was the Gabonese who looked more likely to go ahead during the opening exchanges as Denis Bouanga fired a first-time shot against the crossbar and Pierre-Emerick Aubameyang's follow up header was far too weak.
The first injury of the contest came as a major blow to Burkina Faso with talismanic Jonathon Pitroipa forced off the field in a great deal of pain and was replaced by Prejuce Nakoulma.
Midway through the first-half and it was the subsitute Nakoulma who broke the deadlock as he ran the length of the field to chase a clearance, muscling Obiang off the ball before squeezing it past the goalkeeper.
The lead would not remain in tact going into the break though as the Burkinabe conceded a penalty inside the final ten minutes of the first stanza.
Aubameyang latched onto a through ball ahead of the keeper Herve Koffi and was brought down by the stopper having touched it past him in the box.
The Borussia Dortmund forward dusted himself off to take the spot kick which he dispatched easily into the bottom left corner to restore parity.
In the second half neither side were able to break their opponents down although Gabon, who must face Cameroon in their final group game, came the closest to settling the encounter through Bouanga but he was denied by an excellent save.
Both sides have now drawn their opening two games of the tournament.