Everton went ahead in the ninth minute when Seamus Coleman burst into the area and finished with a powerful strike.
Saints substitute Gaston Ramirez equalised in the 71st minute, beating Toffees goalkeeper Joel Robles, who it appeared should have done better in his attempt to save the effort, with a shot from distance.
The three points mean Roberto Martinez's side are - for a few hours at least - up a place to fourth in the table, while Southampton remain ninth.
More top news
The latest weather for the east with Philippa
The latest weather for the west with Philippa
Scientists in Portsmouth are asking the public to keep an eye on the love lives of lugworms as part of a research project.