Brighton took the lead at the Emirates Stadium when Leandro Trossard turned home a low cross from Enock Mwepu to finish a good move from the visitors.
Arsenal had struggled to create chances but thought they had levelled through a close-range effort from Gabriel Martinelli, only for a lengthy VAR check to cancel out his header.
Brighton doubled their lead through Mwepu’s low drive from the edge of the box following a neat interchange between Trossard and Moises Caicedo.
Arsenal gave themselves hope of salvaging a result as Martin Odegaard’s speculative effort looped up off Danny Welbeck to half the arrears.
The result is a huge blow for Arsenal's Champions League hopes an they have now lost two on the bounce following their 3-0 loss at Crystal Palace last Monday.
For Brighton it was their first win since their 2-0 triumph at Watford way back in February. The win lifts them to 11th in the league standings and in with a chance of achieving their aim of a top 10 finish.
Sonny Turner was at the Emirates Stadium for Sussex World and here's his player ratings
13. Tariq Lamptey- 6
Showed his usual energy, and aided the Brighton right flank in dealing with Arsenal throwing everything at them in the closing minutes.
14. Adam Webster- 6
Added an extra body in the defensive line for Graham Potter’s team, and did well in seeing out the game under immense pressure.