A goal from Aubameyang in the opening ten minutes looked to set Arsenal up for a successful night, but second-half goals from Christian Benteke and Odsonne Edouard turned the tie on its head.
However, the Eagles' excellent response was undone in the dying embers by a last-ditch Alexandre Lacazette dagger.
Arsenal were denied the opportunity to move into the elusive top four, while Crystal Palace maintained their safe midtable spot.
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The match
Returning to the home stadium of the team where he saw his playing days flourish most, Patrick Vieira rocked up to The Emirates without Wilfried Zaha and nothing but a longing itch of chills as he was welcomed with cheers.
However, it wasn't the same welcoming start on the pitch for Crystal Palace, who made a slow start to proceedings, conceding within eight minutes through Pierre-Emerick Aubameyang.
The Congolese striker capitalised on a rebound that followed an acrobatic diving save from Vicente Guaita; his sharp reactions meant he notched his third goal in as many games.
An appeal for a penalty from Christian Benteke was waved away at the other end quickly after, signalling a rare sight of goal for The Eagles in the first 15 minutes.
Following the opener, which saw Arsenal's early perseverance pay off, both teams would go on to have their fair share of possession, but it was the home side that would still look the more fearsome, pulling off several shots from afar that peppered the Palace goal.
The presence of Christian Benteke did, however, cultivate another slight concern for The Gunners, turning inside the area and hitting a strike into Aaron Ramsdale's gloves on the 27th minute, showing glimpses of attacking hope.
Arsenal started to show signs of bedraggled play towards the 34th-minute mark, giving Palace a spell of opportunities. A pull-back from the alert Mitchell reached Edouard, but the striker hooked the ball up and over.
A pinball in the box via a Conor Gallagher corner caused more problems for the Arsenal backline moments before the break. He would then follow up his creativity with a rocket that was well handled by the goalkeeper in added time.
Soaking up the pressure, though, Mikel Arteta's side went into the interval with their noses in front.
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Second half
The second half started almost like the first, with Arsenal causing Vicente Guaita to scramble across his line. Luckily for the Palace shot-stopper, Thomas Partey's speculative effort tipped the crossbar, otherwise, the deficit would have been doubled.
After almost securing the host's second of the game, Partey became the architect to Arsenal's downfalls, gifting the ball to Jordan Ayew, who opted to slide the ball into Benteke.
The high-press from Vieira's Palace paved the way for an easy Benteke goal, as the Belgian slotted the ball into the bottom right with supreme composure.
Being the likely scorers in most of the second halves that they have played, Palace pushed for their first lead of the game after their equaliser. A Jordan Ayew rocket failed to beat Ramsdale, and a succession of corners followed suit.
It wasn't until Alexandre Lacazette's arrival that the home fans kicked into gear, with the Frenchman almost assisting with his first touch. But despite the roars of encouragement, it was anti-climactic.
However, Palace's quick counter-attack was not.
A fast exchange of plays following a remarkable Guaita fingertip save saw Odsonne Edouard smash the ball off the crossbar and into the Arsenal goal, giving Palace the lead for the first time in the tie.
For the rest of the game, Palace invited pressure to their defence. Kieran Tierney smashed the ball off the crossbar, and other attempts followed, but Vieira's men remained tough at the back.
That was until Lacazette scored and snatched a point.
The substitute wheeled away in celebration as he nicked a goal at the death following a setpiece.