Chelsea looked to be in danger of slipping to their first home defeat in the top flight under Jose Mourinho when Jay Rodriguez was gifted an opening goal after only 13 seconds following a bad mistake from Michael Essien.
Essien was making his first Premier League start since May 2012 and after he was substituted at half-time, the midfielder's blushes were spared as Chelsea fought back to secure all three points courtesy of Gary Cahill's first league goal of the season, Terry's towering header and Demba Ba's last-minute strike.
Southampton were forced to give goalkeeper Paulo Gazzaniga his first appearance for a year when Artur Boruc went off with an injury just after Cahill's equaliser and the youngster was beaten by Terry just a few minutes after coming on and then Ba right at the death as Southampton slipped to their second defeat in London in the space of eight days.
Victory for second-placed Chelsea ensured they cut the gap on leaders Arsenal to four points.
Mourinho put Chelsea's poor performance at Basel in midweek down to tiredness and he made four changes to his starting line-up.
Samuel Eto'o was replaced by Fernando Torres up front, while Eden Hazard and Juan Mata joined Essien in the starting line-up as Willian, Frank Lampard and John Obi Mikel dropped to the bench.
Defender Dejan Lovren returned for Southampton at the expense of Jos Hooiveld after missing the defeat at Arsenal last weekend due to illness and striker Pablo Daniel Osvaldo was preferred to Rickie Lambert in attack.
Mourinho would have been eager for Essien to stamp his authority on the game, but the Chelsea boss must have been questioning his team selection once again straight from the kick-off as the midfielder's attempted clearance looped into the air and into the path of Rodriguez, who kept his nerve to beat Petr Cech with a composed right-foot finish after just 13 seconds.
Essien's miserable afternoon continued when he was booked for diving after 32 minutes and Oscar headed straight at Boruc soon after he had picked up an injury that resulted in Lampard replacing him five minutes before half-time.
Boruc made an outstanding reflex save to claw out a Torres header after 43 minutes as Chelsea's frustration mounted.
Mourinho replaced Essien with Ba at the break and Boruc had to be alert once again to tip over Lampard's free-kick, but Chelsea were level after 54 minutes when Ba diverted Branislav Ivanovic's header into the post and Cahill scrambled in the rebound from close range.
That proved to be the end of Boruc's afternoon as he was replaced by Gazzaniga due to injury. And the young Argentinian keeper was picking the ball out of the back of the net just four minutes after coming on, when Terry rose highest to meet Mata's cross and headed into the far corner of the net.
Chelsea stayed on the front foot and Ba flashed a shot wide with his left foot after 71 minutes after shrugging off his marker, but the Senegal striker was not to be denied after 89 minutes when he poked the ball inside the near post with his right foot after great work from Ramires on the left.
