Although defender Rob Holding nearly snatched a stoppage- time winner for Arsenal when he headed against the crossbar, it was another tepid performance by the Gunners who were on the back foot throughout.
The result left Arsenal, who had lost their previous four home games, in 15th place on 14 points from 13 games while Southampton moved up one place to third on 24 points.
He was powerless three minutes later, however, as Theo Walcott scored against his former club to put the Saints ahead with a dinked finish after Che Adams released him through the middle with a defence-splitting pass.
Nicolas Pepe and Bukhayo Saka went close for Arsenal before Pierre-Emerick Aubameyang levelled in the 52nd minute with a clinical finish into the bottom left corner after good work by Saka and Eddie Nketiah.
It seemed Arsenal had gained some momentum but they were pegged back again after Gabriel was sent off for a second bookable foul when he hauled down Walcott in the 62nd minute.
Holding then nearly stunned the Saints as he met an inviting cross from the left with a header that left keeper Alex McCarthy rooted to the line as it rattled the crossbar.