The young Gunners took the lead through Joe Willock’s penalty in the 59th minute but an own goal from Kostas Pileas saw Brighton equalise in the closing stages.
The visitors then took all three points after David Ajiboye’s strike got the better of Arsenal goalkeeper Alex Crean.
Despite the defeat there were some positives for Arsenal, with Yassin Fortune playing 45 minutes on his return from injury and Charlie Gilmour making his first appearance of the season as he completed just over an hour.
However, Nathan Tormey, another player who has had injury problems this season, had to be substituted himself just 13 minutes after coming on as he suffered another setback.
Arsenal: Crean; Osei-Tutu, Ballard, Medley, Pileas; Gilmour, J. Willock; Tella, Coyle, Fortune; Malen.
Subs: Tormey (for Fortune, 46), Omole (for Gilmour, 64), Beckford (for Tormey, 77). Not used: Virginia, Thompson.