Mason Mount’s penalty earned Chelsea a point and preserved their unbeaten record under boss Thomas Tuchel.
Mount netted from the spot 10 minutes into the second half after being brought down in the area by Danny Ings.
The Blues fell behind to a first-half goal scored against the run of play by Takumi Minamino.
The Japan international darted onto Nathan Redmon’s pass, went past Cesar Azpilicueta and then fooled keeper Edouard Mendy with a clever dummy before nonchalantly scoring into an empty net.
Chelsea had most of the possession but were not at their best on what was ultimately a frustrating day against a team that had lost their previous six matches.
And Southampton almost regained the lead when Jannik Vestergaard’s looping header hit the top of the bar.
Chelsea: Mendy, Azpilicueta, Zouma, Rudiger, James, Kante, Kovacic (Jorginho 76), Mount, Alonso, Abraham (Hudson-Odoi 45 (Ziyech 76), Werner.
Subs not used: Kepa, Christensen, Jorginho, Giroud, Chilwell, Gilmour, Emerson.