Adam Lallana and Kelly Youga both tried their luck from distance at either end before Rob Elliot was forced to palm a 35-yard effort from Lloyd James around the post 10 minutes before half-time.
It seemed a matter of if, not when, the deadlock would be broken - and the opener duly arrived three minutes before the interval courtesy of Lallana's third goal of the season.
Wayne Thomas crossed from the right wing and Lallana got ahead of his marker to rifle low past Elliot from 12 yards.
Deon Burton fired Southampton a warning of the threat he still poses after the restart as he drilled wide from 30 yards before hauling Charlton level.
Jonjo Shelvey's cross from the left wing eluded everyone and Burton headed home his second goal in as many games for the Addicks and his fourth in total this term. A scrappy period of play followed the flurry of goals before Youga hit the post with an 18-yard drive with 16 minutes remaining.