Youssouf Hadji gave the home side the lead four minutes before the break but Aubameyang's goal ensured both sides took a point from the contest.
St Etienne started brightly and only a last-ditch tackle from defender John Boye prevented Jean-Pascal Mignot opening the scoring for the visitors in the fifth minute - and soon after Bakary Sako shot powerfully wide.
The home side responded in the 12th minute with Julien Feret winning a duel with Mignot - but Stephane Ruffier came off his line to close down the opportunity.
St Etienne had penalty claims turned down midway through the half when Lynel Kitambala went down in the area under pressure from Jean Kana-Biyik - but no spot-kick was awarded.
Ruffier got down well to deny Feret - but the home side took the lead seven minutes later when Hadji blasted in the rebound after Jonathan Pitroipa's shot had been parried by the goalkeeper.
The influential Feret set up Hadji for a chance five minutes into the second half, which Ruffier saved, then Pitroipa lobbed over two minutes later.
However, St Etienne equalised against the run of play when Fabien Lemoine crossed from the left for Aubameyang to power a header beyond goalkeeper Benoit Costil.
The visitors looked the more likely winners in the closing stages and they were given a chance 12 minutes from time when Chris Mavinga brought down substitute Max Gradel.
Sako's free-kick cleared the wall - but Costil pushed the ball away for a corner.
