The Gabonese forward responded to Christian Pulisic's early opener with a penalty to level and a beautiful wriggle and finish for Arsenal's winner. Chelsea will feel they were out of luck at Wembley, as captain Cesar Azpilicueta and Pulisic were forced to leave the action with hamstring injuries and Mateo Kovacic was controversially dismissed for a second yellow card.
Arsenal extended their record to 14 FA Cup triumphs with the win, and offered tangible evidence they are headed in the right direction under manager Mikel Arteta.
Willian was a surprise absentee in Frank Lampard's 20-man party while N'Golo Kante was on the bench. Willy Caballero kept his place over Kepa Arrizabalaga in the Chelsea goal, meaning he only missed the round of 16 affair with Liverpool during the Blues' FA Cup run.
The match was open straight from kickoff. Aubameyang should've tested Caballero when he headed wide from Maitland-Niles' cross and Mason Mount forced Emiliano Martinez into a save with a shot from outside the area.
Pulisic started and finished the move which resulted in his goal in the fifth minute. The American ran through the center before pushing the ball down an inside-left channel for Mount. Olivier Giroud then tickled Mount's low cross to the onrushing Pulisic, who slipped past Kieran Tierney before confidently lifting the ball over Martinez.
The Gunners restored parity soon after the first water break. Nicolas Pepe's beautiful swerving shot from outside the area was ruled out due to Maitland-Niles being offside in the buildup, but Aubameyang scored moments later from the penalty spot.
Azpilicueta initiated contact with Aubameyang outside the area but the Spaniard held onto the Arsenal striker's shoulder to deny him a shooting opportunity from inside the box. Caballero, a goalkeeper with a fine spot-kick record, was sent the wrong way by Aubameyang.
Chelsea were reeling from another setback when Azpilicueta appeared to pick up an injury minutes after Aubameyang's penalty. The Blues skipper left the field in tears and was replaced by Andreas Christensen.
Lampard's side lacked coordination toward the end of the first half and held on to keep the score level at the break.
Pulisic was the next to fall in the first minute of the second period. He sprinted at Arsenal's goal with red shirts trailing in his wake and steered a shot wide, but replays showed the youngster was screaming through pain during his run. He may have scored if he didn't pick up the injury, and yet another hamstring pull was testing Lampard's resources. Pedro was called off the bench.
Mount was driving Chelsea as his team pushed to regain the lead, but a surging run from Bellerin led to Arsenal's second. Christensen's eventual challenge on Bellerin bounced to Pepe, who passed across the edge of the 18-yard box. Kurt Zouma stood no chance: Aubameyang received the ball, turned the defender inside-out with some slick footwork, and finished with a chipped effort over Caballero.
Aubameyang’s brace at Wembley followed his double in the FA Cup semifinal against Manchester City.
Christensen was left writhing on the turf after his challenge on Bellerin, further underscoring Chelsea’s rough luck, but he was eventually able to continue. Kovacic was sent off when he received a second yellow card for a collision with Granit Xhaka, a dubious decision by referee Anthony Taylor that Video Assistant Referee failed to alleviate.
Chelsea's late attempts to rally were halted in devastating fashion when Pedro appeared to suffer a significant shoulder injury in the final few seconds.
Still, the celebrations in an empty Wembley were audible at the final whistle as Arsenal’s at-times calamitous season ended with silverware.