The Gunners went into the match on a 12-match winning run on home soil, and were on track to extend that when Eddie Nketiah put them in front to make it 11 goals in 12 matches in the competition.
But Danny Welbeck scored from the penalty spot on his Emirates return, before Kaoru Mitoma and Tariq Lamptey struck after the break to send the Seagulls through and halt Arsenal’s charge on all fronts.
Mikel Arteta made ten changes from the side that beat Chelsea at Stamford Bridge, with William Saliba the only player to keep his place, and it perhaps showed as Brighton made the quicker start. Julio Enciso had a big chance in the opening minutes, but made a mess of his header.
The Gunners grew into it though and took the lead, Nketiah once again delivering in the Carabao Cup. Reiss Nelson injected some pace and drive into the build-up, slid the ball through to Nketiah and it was a brilliant curling finish into the top corner.
That lead lasted seven minutes before Welbeck was brought down by Karl Hein, as the Arsenal goalkeeper slipped to commit the foul and concede a penalty. Welbeck made no mistake against his former club as he sent the debutant the wrong way.
Arsenal were well on top immediately after the break, Nketiah hammering an effort against the post and Albert Sambi Lokonga having several efforts at goal, but it was Brighton who scored against the run of play as they broke away on the counter and half-time substitute Kaoru Mitoma produced a lovely finish.
That halted Arsenal’s momentum and they struggled to recreate that pressure, with the task then becoming even more difficult when the Seagulls doubled their advantage. Lamptey beat Nelson for pace and fired a left-footed strike past Hein to leave the hosts with a mountain to climb.
Arteta immediately turned to Gabriel Jesus and Oleksandr Zinchenko, with Gabriel Martinelli already introduced, but the first-team stars could not inspire a comeback as Arsenal fell at the first hurdle in the Carabao Cup.