Marco Arnautovic was guilty of letting his aggression get the better of him and in the 23rd minute lunged in with a dangerous high foot on Sofiane Boufal.
Claude Puel's side dominated possession from this point onwards, something they've done on many occasions this season, but never really looked like scoring - also familiar.
What was really frightening about watching Puel's side was the lack of drive from midfield; when you look at the central midfielders he has at his disposal, it's clear to see why.
Virgil van Dijk looked to take it past opponents, more so than any one of Steven Davis, James Ward-Prowse and the defensive-minded Oriol Romeu.
However the skill-set of these players doesn't allow them to do so, as their qualities lie in passing.
The only time Stoke stopper Lee Grant really had to sweat was when full-back Ryan Bertrand launched a beautifully struck long-shot. Yet the save was equally magnificent.
Apart from that, frontman Jay Rodriguez had a golden opportunity when Boufal slipped him in. The sight of the former Burnley man mistiming his slide was one Southampton fans know all too well.
Not only do Saints desperately need a new forward - more apparent after Austin's injury - they also need to search the market for a goalscoring midfielder.
Rodriguez's lack of sharpness
During an away game with Manchester City at The Etihad in April 2014, Rodriguez suffered an ACL injury - one that ruled him out for around a year.
At the time the £7 million signing couldn't stop scoring; racking up 15 goals in 33 games. His fine form was rewarded when the then-coach of England - Roy Hodgson - gave him his first full international cap.
Rodriguez returned in pre-season of the 2015 campaign for his team's Europa League qualifiers and despite scoring, his overall play seemed sluggish - a far cry from his quick-dribbling and sharp-passing style of before.
Making 12 appearances in the resulting Premier League campaign 'Jay Rod' made no real impact. However his newly-signed four-year-deal in May 2015 meant that when the current season kicked off, he did too despite interest from West Brom.
Although Rodriguez did save a point late on at home in a 1-1 against Sunderland, his start against Arsenal in the next match proved too soon. All game long his sharpness looked way off for a top-tier footballer, punishing the team with a pass success rate of around 66 per-cent.
Three key parts of his game before the injury were his clinical finishing, hold-up play and an ability to out-pace and strengthen opponent defenders. A good example of this is his goal against Liverpool in a 3-1 win at St. Mary's in March 2013 to end the game.
None of these attributes really define Rodriguez anymore; his two goals this season include a goalkeeping mistake (vs. Sunderland) and a tap-in (vs. Sparta Prague).
Of course, under Mauricio Pochettino, Rodriguez was playing a different role on the left wing - something that looks unlikely to happen for current coach Puel.
Lack of confidence for Long
Not only has Rodriguez looked like a shell of himself, striker Shane Long has been nowhere near good enough up until now.
Whether this is down to Long being used in a system that doesn't suit him or a lack of confidence, scoring zero goals with the chances he's had is not representative of his ability.
You can't put it down to the pressure of an expensive price tag anymore; although at £12 million Southampton really did break the bank to become his fifth club; as the striker goes into a third season for his current employers.
Only Graziano Pelle (11) and Sadio Mane (also 11) scored more goals than Long under Ronald Koeman in the league last year.
This was most definitely the Irishman's best spell of his career. He looked settled and confident in front of goal. Before then, finishing was not a key part of his game; work-rate and runs in-behind made up most of Long's manifesto.
Perhaps this was the best Southampton fans will ever see the former Hull forward perform.
Lack of goals from midfield
You'd have to go all the way back to Adam Lallana - now thriving under Jürgen Klopp at Liverpool - when trying to find a true goalscoring midfielder in Southampton's recent history.
Which, when you think about it, is scary. He left the Saints in July 2014, mind.
Saints' current crop of midfielders is one of the better ones in England but when you search for one who has a knack of scoring, Puel's other problem becomes clear.
Ward-Prowse has one goal in the league while his midfield teammates have none. Romeu has never been asked to do so due to his role, possibly having his best season in defensive midfield so far.
Davis' finishing woes will always follow him as his leadership and ability to keep the ball ticking are what shines through.
Signed from Bayern Munich in the summer, Pierre-Emile Hojbjerg started off on the right foot in Southampton's opening fixture, a draw with Watford, where he came off the bench to inject some life into a lifeless midfield.
But since being asked to start in four Europa League group matches, his form has dipped slightly - perhaps from fatigue.
A lot of the time the Danish international picks the ball up on the edge of the box with space, unable to make the most of the opportunity to score.
Nonetheless, at the young age of 21, Hojbjerg will surely be a fan-favourite if he sticks around, his play reminiscent of former Saints captain Dean Hammond - using pure grit and determination. Obviously with a lot more skill at his disposal than the now-free-agent.
Jordy Clasie notched his first goal for Southampton in a 2-0 victory away to Arsenal in the quarter-finals of the EFL Cup. His place lies deep in the midfield, similar to teammates such as Romeu, Prowse and Harrison Reed - an academy graduate who signed a long-term contract yesterday.
The fact that Jake Hesketh is probably Puel's most attacking midfielder should be a worry for him. Hesketh also put pen-to-paper earlier this week, but has barely featured in the league for Southampton in his short career.
Although, the Frenchman loves to dip into the academy for squad depth - one thing that you couldn't say for Koeman. With Hesketh, you're getting the potential of possibly another Lallana (no pressure).
Should Puel bring back a familiar face?
Before his forced departure to Manchester United, Morgan Schneiderlin showed signs of maturing into a more well-rounded midfielder.
Schneiderlin was extremely vital in Southampton's rise to the Premier League, playing in midfield with Hammond they served as protection: allowing talented forwards like Rickie Lambert, Lallana, Alex Oxlade-Chamberlain and at a stretch, Guly do Prado to flourish and make goals.
However, it wasn't until his first year in the top-tier that he showed a goalscoring threat, scoring only three goals in his previous four seasons.
The French defensive-mid showed he can actually be a threat, grabbing 11 goals in three years at the highest level.
Even his attitude towards attacking changed as passes that would normally be played sidewards started to become more forward-thinking - possibly as result of having the powerful Victor Wanyama next to him.
Jose Mourinho doesn't seem to have the French international in his plans, having only started eight games in all competitions.
So why shouldn't Southampton make a move to bring him back?
Fans of the South Coast club would welcome Schneiderlin back every day of the week.
What will Puel decide?
The month of January will not go by without drama for Puel, every week a rumour of a new signing will mean most press conferences are dominated by transfer related questions.
Either Southampton can try the market, or stick by their academy.
Josh Sims has already shown signs of being a bright spark, Hesketh similarly. Sam Gallagher is currently out on loan at Blackburn, where the goals seem to consistently follow him.
Bringing him back might show some desperation from the club whilst also acting as a sign of disrespect to more senior strikers in Rodriguez and Long.
Just looking at Southampton's striker situation is the equivalent of not seeing the wood for the trees.
If fans only see the goals coming from the forwards - as that's been the case for many years - then they're inclined to believing that's the only position they're meant for.
When in fact the modern game allows for more goalscoring threats in midfield; defenders scout the opposition's attack, but do they scout three opposing midfielders?
For teams facing Puel's side, it's become all too easy. Wednesday night was a great showing of how to defend against Southampton, flooding the middle with tall defenders; allowing wingers and full-backs the time to cross into marked strikers or unimposing wingers like Nathan Redmond.
At some point, there has to be a 'Plan B', either a more creative striker or a taller one. Or instead, finding goals from the gaps left in midfield must be the answer to Southampton's toothless attack.