Amadou Onana’s first Everton goal was not enough as a James Ward-Prowse double condemned the Blues to a 2-1 defeat at Goodison Park.
Frank Lampard’s side looked on course for a precious victory when midfielder Onana headed home Demarai Gray’s corner six minutes before half-time.
But Ward-Prowse levelled matters seconds after the interval, collecting Che Adams’ flicked header to finish inside the area.
And the Southampton captain grabbed the winner 12 minutes from time with a 20-yard free-kick.
Lampard made just one change to his line-up from the XI who performed so well in the FA Cup tie at Manchester United eight days earlier, with Dominic Calvert-Lewin leading the attack ahead of Neal Maupay.
It meant Alex Iwobi – taken off on a stretcher at Old Trafford with an ankle ligament injury – made a speedy and welcome return in midfield alongside Onana and Idrissa Gana Gueye.
With Iwobi back, there was concern Everton would lose a different player to injury just seconds into the contest when Ben Godfrey went down after making a clearance. Thankfully, after treatment, though, he was up on his feet again and able to take his place in a three-man central defence alongside Conor Coady and James Tarkowski.
Iwobi was in the thick of the early action and, on 10 minutes, he threaded a ball to the right wing for Seamus Coleman to do well to turn Kyle Walker-Peters and get dragged down by the defender. The Blues couldn’t capitalise on Gray’s whipped free-kick from 20 yards, however.
Goodison was at its vocal best moments later as Walker-Peters looked to move into the Everton area after a Southampton counter, only to be stopped in his tracks with a perfectly-timed slide tackle from Onana.
The Blues soon threatened with quick counters themselves, Gana and Onana exchanging passes before the Belgium international was chopped down on halfway by Romeo Lavia for the match’s first booking.
Gray then sprinted through the middle of the park and just delayed his pass wide left, enabling Ibrahima Diallo to make a crucial tackle.
The best move of the early stages came on 20 minutes as Mykolenko slid through a pinpoint pass to Gray on the left edge of the area, where the in-form forward took the ball past keeper Gavin Bazunu and squeezed his finish over from a tight angle.
Everton were by far the brighter side but the visitors showed their threat just before the half-hour mark when Mohamed Elyounoussi was in space inside the right of the Blues’ area and saw his effort hit Mykolenko and deflect just past the post.
From James Ward-Prowse’s resulting corner, Pickford then had to punch away Mohammed Salisu’s header.
A lull in play quickly sprung into life with the opener on 38 minutes, with Gray – so influential in recent weeks – at the heart of it.
First, the 26-year-old jinked one way and then another to earn a corner off Walker-Peters and, as he whipped in a teasing set piece, Onana was on hand to plant home a header from 10 yards out for his first Blues goal.
Goodison burst into life and it was so nearly 2-0 shortly after as Gana robbed Lavia of possession, fed Calvert-Lewin who sent Iwobi racing down the left channel, the Nigerian cutting inside and firing a 20-yard shot inches past the far post.
Instead of 2-0, it was so nearly 1-1 with nearly the last kick of the first half, Southampton’s fast counter ending with Ward-Prowse placing a low shot into the bottom left-hand corner that Pickford did superbly well to tip on to the post and out for a corner.
Ward-Prowse was not to be denied seconds after the restart, however. Che Adams flicked down a high ball, allowing the Southampton corner to collect inside the area and finish past Pickford.
The setback rocked the Blues but they were the next team to knock of the door as Iwobi outmuscled Samuel Edozie, passing inside to Gray whose low 25-yard was held by Bazunu.
Lampard’s men went agonisingly close to retaking the lead 10 minutes after the restart, Godfrey squaring to Calvert-Lewin and the England striker watching his finish from the edge of the area deflecting off Edozie and beating Bazunu, only to bounce back off the bar, on to the goalline and out.
Both teams pushed for a winner to ignite their seasons, leaving spaces at the back and it needed a solid block from Coady to deny Adams as he shot from the right edge of the area.
Onana was the constant threat for the Blues, popping up everywhere over the park and orchestrating a counter from the edge of his own area, striding upfield before being taken down by Diallo as he looked to put Calvert-Lewin clean through.
The Southampton midfield was rightly shown a yellow card and, moments later, Gray swung a deep cross in from the left that Godfrey turned on to the side netting.
The chances kept on coming for Everton, Calvert-Lewin racing past Lyanco and cutting back a pass inside that area that ended with Godfrey booming a finish just wide.
A winning goal felt inevitable. Having done so much to be the ones to get it, though, Everton were undone by a cruel suckerpunch 12 minutes from time. Another Southampton counter ended with substitute Anthony Gordon being penalised for a barge on the edge of the area and Ward-Prowse sent the free-kick over the wall and into the net.
Ellis Simms was brought on for Gana as the Blues pushed for a leveller. It nearly came in four minutes of added time as Gordon cut back from the byline, Bazunu punched out and Tarkowski’s goalbound shot was deflected behind by Walker-Peters.
But that was as close as Everton were to get on a bitterly disappointing afternoon at Goodison.