Arsenal frantically searched for a winner but Aubameyang volleyed wide from seven yards out and Brighton keeper Mat Ryan made a series of fine saves.
Pascal Gross could have won the game for Brighton late on but skewed his effort out towards the sideline with the goal unmanned after Bernd Leno's superb save from March, while the visitors withstood another flurry from Arsenal in the final stages.
Sloppy Arsenal fail to scrape through
Looking to avoid a fourth straight Premier League defeat, Arsenal made a bright start in attack, though were fortunate to be awarded a penalty, despite referee Anthony Taylor being well placed, with replays showing Jahanbakhsh got to the ball before Monreal fell.
Still, an early lead through Aubameyang's 20th league goal of the season should have allowed the hosts to exert control over the game, but instead they became nervy and vulnerable.
Goalkeeper Leno sent an abysmal clearance straight to March before recovering to save Murray's free header moments later, while Stephan Litchtsteiner, making his first appearance since late February, was frequently exposed.
There was another promising spell at the end of the first half, with Aubameyang, Shkodran Mustafi and Henrikh Mkhitaryan testing Ryan, but Arsenal's inability to create clear chances gave Brighton increasing confidence in finding an equaliser.
Even then it took a staggeringly poor decision by Xhaka. Running behind the surging March inside the area, the Switzerland midfielder initially held up his hands to indicate he was not touching the Brighton forward only to then whack his shoulder and concede a penalty.
And so a game Arsenal should perhaps have dictated against an opposition who were already guaranteed Premier League survival became a manic attempt to salvage a dispiriting end to the league season.
They came close to scraping a winner but could not do it, the lap of honour conducted with glum faces as the Gunners must now focus on winning the club's first European trophy since 1994.
