Former Gunner Theo Walcott put the visitors ahead with a superb lifted finish after being slipped through by Che Adams, but Pierre-Emerick Aubameyang ended his longest run without a Premier League goal with a cool finish after magnificent work from Bukayo Saka.
At that point in the second half, it was the home side who were in the ascendancy and looking the more likely winners.
However, their momentum was checked when Gabriel was shown a second yellow card for hauling Walcott down and, just as had been the case when Granit Xhaka was sent off against Burnley on Sunday, the tide turned.
Southampton pressed for a winner and substitute Nathan Redmond came closest to finding it, striking the bar at full-stretch after a terrific pass form Oriel Romeu.
Arsenal still had a late chance to win it deep into stoppage time but Rob Holding’s excellent header from Saka’s free-kick came back off the woodwork with the goalkeeper well-beaten.