Neal Maupay scored for his side to make a remarkable comeback for Brighton who came from a goal down to seal a win.
Nicolas Pepe had fired the Gunners into a lead in the 68th minute with a superb curling shot to make it 1-0.
However, Lewis Dunk equalized for the home side in the 75th minute from close range to make it 1-1 before Neal Maupay sealed it in the 95th minute.
A loss on Saturday evening means that Arsenal have now lost back-to-back games since the Premier League returned.
They resumed with a 3-0 loss against Manchester City on Wednesday night.
Champions League qualification difficult for Arsenal
Arsenal’s loss means that their UEFA Champions League qualification dreams have continued to reduce as they remain ninth with 40 points on the log.
To make matters worse, they will be without their goalkeeper Bernd Leno for the remainder of the season through injury.
The German custodian was stretchered off after landing cumbersomely on his ankle in the first half of the game.
Leno collided with Maupay unbalanced and he landed awkwardly on his right leg.
Bernd Leno joins defender Pablo Mari and midfielder Granit Xhaka on the sidelines, both of whom were injured in Wednesday’s 3-0 loss at Manchester City.
A win left Brighton and Hove Albion 15th with 32 points on the log five points ahead of the relegation zone.
Brighton (4-2-3-1): Ryan; Schelotto (Montoya 71′), Webster, Dunk, Burn; Propper, Bissouma (Mac Allister 90+4′); Mooy (March 45′), Gross (Connolly 71′), Trossard (Stephens 87′); Maupay
Arsenal (4-3-3): Leno (Martinez 40); Bellerin, Mustafi, Holding, Kolasinac; Guendouzi, Saka (Tierney 87′), Ceballos (Willock 88′); Pepe (Nelson 87′), Lacazette (Nketiah 78′), Aubameyang