They eventually took a deserved lead in somewhat fortuitous fashion midway through the half, as Kyle Walker-Peters’ shot across goal was flicked beneath Bernd Leno’s dive and into the far corner by Gabriel Magalhaes, stretching to make a block. Danny Ings then saw a goalbound effort blocked and a header fly off-target as the Saints onslaught continued to the break.
Arsenal sparked into life in the closing stages but they created very little in truth and Saints remained a threat on the break, with Nicolas Pepe being denied by Fraser Forster and Ings firing straight at Leno in the best of the late chances.
Here are five things we learned from the fourth-round clash at St. Mary’s.
Hasenhuttl’s incredible job
The Southampton boss has certainly had plenty of plaudits over the last year or so, yet it still probably isn’t enough to fully state the scope of the job he has done.
Saints are one of the best-organised sides on and off the ball, with a clear style and build-up play approach, players who fit the systems employed and everyone works hard to maintain positional balance when under pressure.
They are of course not perfect, and a tendency to sit off when holding a lead has undone them at times this season, but visually and tactically they are an excellent side who play enjoyable football and can challenge the best teams on a one-off basis.
Saints up for the cup
Continuing with the theme of the manager, it was very clear from the fact he sent out his first-choice line-up that Saints feel they can go deep in the competition and perhaps win the FA Cup.
The last time they did so was 1976. Since then they have runners-up once and in the League Cup a couple of times, as well as even finishing second in the old Division One - but silverware has eluded them, outside of the minor EFL Trophy won during the bad old days down in the third tier.
While the likes of Man City, the winners of Man United and Liverpool, or Tottenham will still be among the favourites, Saints also know they’ll have their eyes on bigger prizes - so an upset could easily be on the cards.
Perhaps this is the year they have the depth and consistency to end their long wait for a major honour.
The Gunners have had a marginal upturn in fortunes of late, but here they were blunt, unimaginative, disappointing.
A couple of attacking absences seem to impact their style as much as their substance; without Emile Smith Rowe, rested, and Pierre-Emerick Aubameyang, absent with a personal matter, they managed just two shots on target all game despite lots of late huff and puff to get the ball moving quicker.
In addition, the midfield looked utterly incapable of matching Saints for work rate or ball manipulation until Thomas came on in the second half.
Six unbeaten, and the reign of being cup holders, came to an end with something of a whimper.
Ward-Prowse shines again
The battle for England’s right-back berth seems to be the most-discussed position for Gareth Southgate, but if form plays a big part in his ultimate choices for the Euros in the summer then James Ward-Prowse has a great chance of starting in midfield.
There are other candidates, but few who show the game-to-game levels of both ability and availability that the Saints man offers.
Here once more he was near his best both with ball-winning and protecting the defence, and with distribution and putting the team on the front foot.
He’s indispensable for them and among the most well-rounded central players in the league.
Re-plan and reset
Three days from now, they get to do it all again.
The Gunners are back at St. Mary’s on Tuesday night, with Saints hosting Mikel Arteta’s team in the Premier League.
One place in the table and two points separate the sides, with Saints also having a game in hand. On the evidence of the gap between the teams in the first half in particular, Southampton will be hugely confident of extending that gap, with a win against a top-half rival of some importance if they have aspirations to reach the European spots.
It will arguably be an even more intriguing insight as to where these sides are and it would take a brave person to suggest the Gunners go into the game as anywhere near favourites.