Tom Davies deflected strike in stoppage-time cruelly denied Southampton a priceless win at Goodison Park.
Substitute Nathan Redmond had given Saints the lead with a downward header on 56 minutes with a victory putting them in 16th place.
However, the Everton man had something to say about it when his shot from the edge of the box struck Wesley Hoedt, giving Alex McCarthy no chance.
The goal came with 95 minutes on the clock despite the fact there were four added minutes, leaving Mark Hughes raging at referee Jonathan Moss at the full-time whistle.
Earlier, Charlie Austin forced Jordan Pickford into a good save with a stining volley in the first-half.
After the break, Redmond got on the end of Cedric Soares’ cross following a swift counter-attack.
Maya Yoshida was given his marching orders on 84 minutes after mistiming a 50-50 challenge on Oumar Niasse.
Saints keeper Alex McCarthy made a wonderful save to deny Leighton Baines in the 90th minute but he could not do anything about Davies’ effort, leaving every Saints player dejected.
The draw does see Southampton out of the relegation zone on goal difference ahead of their crucial encounter at 18th-place Swansea on Tuesday night.
Everton: Pickford, Coleman, Jagielka (Klaasen 80), Keane, Baines, Schneiderlin, Gueye, Davies, Bolasie (Funes Mori 45), Vlasic (Niasse 58), Tosun
Subs not used: Robles, Martina, Kenny, Baningime
Southampton: McCarthy, Cedric, Hoedt, Yoshida, Bednarek, Bertrand, Romeu, Hojbjerg, Lemina (Redmond 45), Tadic (Ward-Prowse 70), Austin (Long 76)
Subs not used: Forster, Stephens, McQueen, Ward-Prowse, Long, Gabbiadini