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Goals by Demba Ba and Eden Hazard put Chelsea in complete control of the game at Stamford Bridge but substitute Rickie Lambert and Jason Puncheon struck in the second half to stun the hosts.
Chelsea stayed third in the standings, six points behind second-placed Manchester City and 13 adrift of leaders Manchester United but used up their game in hand. Southampton remained 15th, three points above the relegation zone.
"We have to be more clinical when we have chances," interim manager Rafael Benitez told the BBC. "We have to manage the game, score the third goal and finish the game but we did not do it. We had a lot of chances again, even at 2-0 up, but we did not take them.
"We are in the top three so we will try to be as high as possible, then try to think about the next game."
Chelsea's revival under Benitez looked certain to continue when striker Demba Ba continued his prolific start at the London club with an acrobatic volley in the 25th minute.
Eden Hazard doubled Chelsea's lead just before halftime, side-footing the ball neatly home after Ramires's thumping shot had hit the crossbar to put his side firmly on course for their sixth win in the last seven league matches under Benitez.
But Southampton substitute Rickie Lambert pulled one back with a bullet header after 58 minutes and Puncheon lashed in a fine volley 15 minutes from time to earn the away team a point.
"We came with a gameplan," Southampton manager Nigel Adkins said.
"Chelsea are a good side, we came to block them, deny them space and counter-attack. To go two goals down, when we could have cleared both, was a blow but we showed great character in the second half - great credit to my players."