Michael Ball was Everton's one-hit wonder with a successful single which left Saints wondering how they failed to win this game.
His penalty equaliser 10 minutes from time was the Merseysiders' only serious attempt on goal all afternoon, but it was enough to deny Glenn Hoddle's men a second successive away win.
It cancelled out a stunning 25-yard strike by Jason Dodd just five minutes earlier which looked to have given his side the win they deserved.
On a wretched afternoon, it was Southampton who provided the only bright moments as they outplayed the home side for long spells.
They shut out the Toffees with the kind of new-found resilience which has seen them lose just twice in 10 away matches since they were thumped 7-2 at Tottenham in March.
But for the third time in five games on the road they failed to hold on to a lead when in full command.
It meant that they came away bitterly disappointed with a result they would gladly have taken before kick-off.
That is now a minimum of six points they have thrown away this season, enough to lift them to fourth place!
Instead they are still looking anxiously over their shoulders, their frustration increased by the knowledge that they are so tantalisingly close to getting it right.
The game plan worked almost to perfection as Southampton stifled Everton from the start, drawing the sting from the game and increasing the frustration of the Goodison fans who had not had a victory to cheer since August.
The back four gave solid protection to Paul Jones, diving in with tackles and blocks to ensure he had only a few straightforward crosses to claim.
Dodd and Wayne Bridge let little through on the flanks, while Claus Lundekvam knocked away everything in the middle despite playing with a fractured cheekbone.
The midfield ran like a well-oiled machine. It was five-strong when the home side had the ball with Hassan Kachloul and the tireless Kevin Davies dropping back to bolster numbers and ensure the opposition had no room to play.
But when Saints had the ball, the wide pair pushed on strongly in a fluid system which unsettled Everton who found no rhythm or momentum with Paul Gascoigne ineffective against the sound man-marking of Trond Soltvedt.
Gazza badly wanted to prove a point to Hoddle in their first football meeting since the Saints boss left him out of the England squad for France 98.
But although he showed his undoubted quality with the occasional flash or piercing ball, he only re-emphasised that he is a fading force.
With Gazza under lock and key, Everton lacked any real creative spark in midfield where Chris Marsden ruled the roost and Matthew Oakley again acted as a central cog.
All that was lacking, again, was the killer touch in the final third as Saints once more struggled to turn possession into goals.
Having taken complete charge, they needed a break-through to compound their control and to completely undermine the Blues and their fans who were already on their backs.
And if a flying header by Tahar El Khalej had been two inches lower in the final minute of the first half then Saints may well have won by a distance.
Two weeks ago Ipswich scored at the same stage of the game and went on to beat Walter Smith's demoralised side 3-0.
This might have been a similar crushing blow but the Moroccan's header hit the top of the bar and Everton made the most of the reprieve.
They tried to counter the Southampton shape by switching to a flat back four after the break and withdrawing former Saints striker Mark Hughes, who had got little change out of his old team-mates.
The darting runs of Joe-Max Moore presented different problems, but Hoddle's men stuck to their task with resilience and concentration.
The bite and snap in midfield, coupled with a ferocious work-rate to close down every opening, meant that the Merseysiders frequently gave the ball away.
The home crowd showed their frustration at what was perceived to be a lacklustre and sloppy performance by their team, with Saints getting no credit for their diligence and determination.
Chances were few and far between until Dodd hit a goal quite of context in a drab spectacle. Matthew Oakley's long throw was only half-headed clear and the Saints skipper rammed in a stunning volley. Paul Gerrard got his hands to it but was beaten by the power.
Since Everton had yet to muster a real goal attempt, it looked as though the three points should be secure.
But with 10 minutes remaining Thomas Gravesen crossed from the right for Alex Nyarko who had space to shoot and was just about to let fly when he was felled from behind by Davies.
He may well have scored anyway but Ball sent Jones the wrong way from the spot with Saints grateful that further punishment was not inflicted by referee David Elleray. He could have dismissed Davies who had already been booked for a similar lunge.
It was a shattering blow, but at least Saints did not fold as they might have done in the past. They recognised that they still had what they came for and made sure they protected it.
Instead of trying to regain the lead and possibly leaving gaps for a rejuvenated Everton side, they simply tightened their stranglehold.
Despite the urgent cries from the home crowd, there was no late onslaught to worry about as Hoddle's men saw out time for a point they would have taken before kick-off.
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