Chelsea had been ahead after just five minutes through Christian Pulisic.
But things went from bad to worse for Frank Lampard’s side with three injury setbacks and a red card helping hand the trophy to the Gunners.
After Pulisic’s early opener, Aubameyang levelled with a penalty kick he had won himself on 28 minutes and then brilliantly added his second midway through the second half.
Chelsea then had Mateo Kovacic sent off as they chased the game, the Croatia international picking up two bookings, with the second a controversial call from referee Anthony Taylor.
For Mikel Arteta, this was a first piece of silverware in a managerial career that only began in December and ensured Arsenal will take their place in the Europa League next season.
ubameyang had began his evening by wasting the first chance of the final, heading wide when picked out in the box by Ainsley Maitland-Niles.
Chelsea had their own opening moments later, Xhaka robbed of the ball and Mason Mount’s curling effort forcing Emiliano Martinez into an early save.
But there was nothing the Arsenal goalkeeper could do from the next Chelsea attack as Pulisic struck.
Mount broke into the penalty area and squared to Olivier Giroud, the former Arsenal man flicking the ball into the path of Pulisic, who skipped past the challenge of Kieran Tierney to become the first United States international to score in an FA Cup final.
Azpilicueta would last less than five minutes longer, forced off with an injury as he made way for Andreas Christensen.Arsenal dominated the remainder of the first half without managing to test Willy Caballero in the Chelsea goal.
After the break, Pulisic broke forward looking to add his second of the afternoon but instead was soon going the same way as his captain, limping off with a hamstring injury after shooting wide.
Pedro entered the fray in his place as Chelsea started to wrestle back control of the contest. That was until Aubameyang struck once again.
Hector Bellerin burst forward down the right and Christensen’s heavy challenge saw the ball break to Pepe, his pass picked up by Aubameyang who turned on to his preferred left foot to lift the ball over Caballero.