Not even a quite breathtaking penalty save from Christian Walton could prevent Wigan Athletic crashing out of the FA Cup to Premier League Southampton.
But the scoreline was hugely flattering to the visitors, who were on the back foot for the majority of an enthralling quarter-final tie.
Latics were made to pay for failing to make the most of their first-half dominance, as the Saints raised their game in the second period.
The visitors took their lead just before the hour mark when, after Walton had brilliantly tipped over an effort from Pierre-Emile Hojbjerg, he was unable to prevent the same player converting from the resulting set-piece.
It looked curtains for Latics with 19 minutes to go when Manolo Gabbiadini raced clean through only to be tripped by Dan Burn as he pulled the trigger.
Referee Michael Oliver immediately pointed to the spot, but Walton pulled off a phenomenal save - diving full-stretch to his left - to keep out the Italian’s penalty-kick.
However, despite the introduction off the bench of Nick Powell, Latics couldn’t find the goal they needed to take the game to extra time.
And they were done by a classic sucker-punch in stoppage-time as Cedric Soares raced through down the left before converting past an exposed Walton.
The setback, while painful, could end up working in Wigan’s favour as far as their major goal for the season - winning promotion back to the Championship - is concerned.
And Paul Cook will know that, if they play for the rest of the season as they did here - especially in the first half - they should have few problems in securing a top-two finish.
Right from the off, Cook’s men showed no fear as they took the game to their visitors, who were being managed by Mark Hughes for the first time.
Playing into quite a breeze in the first half, Latics threatened first with Gavin Massey firing over and Will Grigg seeing a shot deflected behind for a corner.
At the other end, Latics had a slight scare when Walton failed to deal with a routine free-kick, but thankfully gathered the follow-up shot.
Latics came within inches of taking the lead when, after Nathan Byrne’s shot deflected into his path, Chey Dunkley couldn’t quite get a toe to the ball from six yards.
After good work from Grigg and Massey, the ball was half-cleared to Gary Roberts, who tried to lob the ball home rather than put his foot through it, and it sailed over the bar.
Roberts and Grigg then turned down chances to shoot only to see the ball cleared, before a corner from Power from the left almost curled in, before being tipped over by Alex McCarthy.
A lovely cross from Jacobs was only inches in front of Grigg, who would have had a tap-in, and the only complaint at the interval was the lack of a Latics goal their play undoubtedly warranted.
Jacobs fired just over shortly after the restart, but Southampton were suddenly looking increasingly dangerous on the break.
A Saints free-kick from Dusan Tadic landed on the roof of the net, before an awful mistake from Byrne almost gift-wrapped the visitors the opener.
After dribbling it out of defence, Byrne then turned and plays a blind backpass, straight to Gabbiadini, who couldn’t believe his luck.
Thankfully for Latics, a great save from Walton bailed out his mate, and the on-loan Brighton goalkeeper repeated the trick when Hojbjerg somehow got free from a corner.
Unfortunately, the warning wasn’t heeded, and from the resulting corner, Hojdberg again found himself unmarked, and this time planted the ball home from close range.
The Wigan response was to send on Nick Powell and Ryan Colclough for Massey and Roberts, but it was almost game over when Gabbiadini raced through and was brought down by Burn for a stonewall penalty.
The Italian hit the ball with everything he had, right in the corner, but Walton threw himself to his left and somehow tipped the ball away at full stretch.
Boosted by the let-off, Latics pushed forward and, after Powell scuffed a shot towards Grigg, the striker couldn’t get a decent connection from six yards.
Wigan’s final change saw Byrne replaced by Noel Hunt, which meant Power switching to right-back with 10 minutes to go.
Southampton had sent on Shane Long by the point, and the new-boy thought he’d made the game safe when he was played through, and struck a decent-enough shot.
However, with the flag up in any case, Walton pulled off another fabulous save.
With the fourth official signalling four additional minute, Hunt was presented with the ball in the Saints six-yard box, but he couldn’t convert.
And with Latics throwing everyone forward in search of an equaliser, they were done by a classic sucker-punch at the other end through Soares.