The Seagulls extended their unbeaten run to five league games and in doing so heaped more misery on the struggling Gunners.
Albion matched a top-flight record of three consecutive home wins thanks to goals from captain Lewis Dunk and inform striker Glenn Murray, both in the first half.
The result moved Chris Hughton's side up to tenth in the table, seven points clear of the bottom three, while in the opposite camp, the result put more pressure on Gunners boss Arsene Wenger.
Albion boss Hughton named an unchanged starting 11 from last week's 4-1 win against Swansea. The Gunners made three changes with Jack Wilshere, Alex Iwobi and Calum Chambers all coming into the team for Aaron Ramsey, Danny Welbeck and Hector Bellerin.
In the early exchanges, Mesut Ozil put a left-footed curler over the bar and Dunk had a nervy moment, diverting Henrikh Mkhitaryan's cross narrowly over his bar.At the other end, Ezequiel Schelotto's cross was flicked wide by Jose Izquierdo via a deflection.
But from the resulting corner, Albion led. A towering Shane Duffy header back across the box fell to his fellow centre-back Dunk, who swept home.
The hosts looked to add to their advantage with Arsenal seemingly creaking and Pascal Gross forced a low save from Petr Cech.
Dunk put another header over the bar, before on 20 minutes it should have been 2-0. Anthony Knockaert dispossessed Alex Iwobi and Gross drove into the box to flick back to Knockaert, but the winger shot straight at Cech.
Albion, however, only had to wait six minutes for their second. A delightful cross by Gross saw Murray leap highest, virtually unchallenged in the box and it slipped through Cech's grasp and found the back of the net.
To demonstrate Albion's dominance, Maty Ryan touched the ball for the first time on 30 minutes with a routine stop. While at the other end, Murray almost latched onto a teasing Knockaert free kick, but Cech collected at the second attempt.
Arsenal pulled one back on the stroke of half-time as Aubameyang stuck out a boot deep inside the box to turn home Granit Xhaka's pass.
And it could have been 2-2 moments later as Laurent Koscielny's header crashed back off the bottom of the post, but Albion held out until the break.
The first action of the second half came after nine minutes as Cech awkwardly put behind Schelotto's cross, but the resulting corner was cleared.
Ryan then collected a low Iwobi shot, before moments later producing an excellent full-length diving save to turn Ozil's shot behind. An already booked Xhaka then went down in the box, but the penalty appeals were waved away.
Aubameyang then rounded Ryan, but the keeper got a hand to his ball back across the box and a nervy moment was cleared.
A lengthy delay then ensued as Schellotto collided horribly with Sead Kolasinac and there were immediate fears for the Albion midfielder, who at first look to be unconscious, but eventually he was able to walk off the pitch and was replaced by Bruno. Somehow the Arsenal player also escaped without a second booking.
Albion could have had a third shortly after play resumed as Izquierdo broke forwards and ran at Shkodran Mustafi, but fired just wide.
The hosts had the ball in the net on 83 minutes as Murray tapped in Izquierdo's square ball across the box, but the midfielder had strayed offside in the build-up.
With seven added minutes after the Schelotto injury, Arsenal's best chance of a leveler fell to Aubameyang in the box, but he fired straight at Ryan on the turn.
Albion: Ryan, Bong, Dunk, Duffy, Schelotto (Bruno 69), Knockaert (March 76), Stephens, Propper, Izquierdo, Gross (Kayal 86), Murray. Unused subs: Krul, Goldson, March, Ulloa, Locadia.
Arsenal: Cech, Chambers (Bellerin 83), Koscielny, Mustafi, Kolasinac, Ozil, Wilshere, Xhaka, Iwobi (Welbeck 73), Mkhitaryan (Nketiah 83), Aubameyang. Unused subs: Ospina, Holding, Maitland-Niles, Elneny.
Referee: Stuart Attwell.