The Blues led at half-time courtesy of goals from Demba Ba and Eden Hazard and they appeared to be cruising to a first home win since December 23.
But Rickie Lambert pulled Southampton back into the game with a header three minutes after coming off the bench and Jason Puncheon equalised with a brilliant volley.
Since their 8-0 rout of Aston Villa, Chelsea have lost at home to QPR and Swansea and now drawn with the relegation-battling Saints.
Benitez, booed by supporters on the final whistle, admitted Chelsea had thrown away the chance of victory by failing to kill off the game.
"We should have won," Benitez said. "We didn't take our chances when we had them. I said we would have to be more clinical and this was the same.
"We had situations where we could score. We didn't and they broke on a counter-attack. We gave them hope they could score and they did it.
"I was talking to the team at half-time, trying to say `we have to score a third goal'. I think for us we cannot be happy drawing at home. I am disappointed. When you know your players and what they can do it is disappointing."