Danny Ings scored in the 25th minute to give Saints a 1-0 lead, and Hasenhuttl’s men comfortably held the advantage until Wolves were awarded a second-half penalty when Ryan Bertrand blocked Nelson Semedo’s attempted cross with his arm.
The point of contention was whether the left-back’s arm was in an unnatural position. The VAR team, led by official Martin Atkinson, saw no need for the on-field referee to reconsider his initial decision to award the kick.
Ruben Neves scored from the spot before Pedro Neto produced a dazzling winner for the visitors.
“I am normally a big fan, and if the VAR followed the rules everything would be easy,” said Hasenhuttl, whose side slumped to their sixth successive Premier League loss.
“I don’t know what Mr Atkinson saw today, but they are not doing a good job at the moment. It is that simple. VAR is destroying the game, that’s right.
“The referee explained that the arm was stretched away from the body. But when the ball hit the arm it stretched the arm away for me.”
The Austrian manager then questioned an incident at the other end of the pitch when a cross struck the arm of Wolves’ Leander Dendoncker, which referee Graham Scott and the VAR team this time declared legal.
He added: “I haven’t spoken with the VAR because he isn’t at the stadium so we can’t.
“This is the issue: the games aren’t decided in the stadium any more, the games are decided at Stockley Park. This is not so good for the game I don’t think.”
The match was a tale of two halves, with the visitors improving markedly as an attacking force after the break.
The home side controlled the opening period and took the lead when Ings scored with a brilliant volley after he was picked out by Stuart Armstrong.
The game turned seven minutes into the second half when Neves converted from the spot. Wolves, buoyed by the goal, went on the front foot and took the lead when Neto jinked his way past Jannik Vestergaard before threading his angled strike between Jan Bednarek and keeper Alex McCarthy.
Saints pressed for an equaliser but were thwarted by Wolves stopper Rui Patricio who made a double save from James Ward-Prowse and Che Adams.
Wolves go 12th in the Premier League table, a point and a place above Southampton.
Contentious decisions irk any team, but it prickles that little bit more when you are desperate for a point, never mind a win.
In the split second Bertrand turned his back to avoid getting struck in the face by Semedo’s cross, he cannot have imagined that referee Scott would point to the spot.
Hasenhuttl’s side never recovered from that as the frailties in defence that have cost them so dearly in the recent past resurfaced. As brilliant as Neto’s strike was, could Vestergaard have blocked his run? And should McCarthy have been beaten from such a tight angle?
It is a shame for the Saints because early in the match they displayed the kind of dominance that saw them beat Wolves in the FA Cup on Thursday.
Ings along with Stuart Armstrong and Nathan Redmond looked formidable in attack and his opening strike was typical of him – instinctive and creative. It was his 30th Premier League goal since the start of last season, and only Liverpool’s Mohamed Salah (36), Leicester’s Jamie Vardy (35) and Tottenham’s Harry Kane (31) have managed as many.
The forward’s progress has been blighted by injuries in recent years, but if he stays fit Hasenhuttl’s side should be able to escape this rut.
This result should settle Wolves fans’ nerves. That is now seven points in the past three league games, which perhaps proves to the team they can still churn out wins without leading striker Raul Jimenez, who continues his rehabilitation following his head injury.
The visitors sat too deep in the first half but manager Nuno Espirito Santo tweaked the system for the second period, with wide men Semedo and Adama Traore beginning to take more risks.
Neves has arguably been Nuno’s most valuable player in attack in the absence of Jimenez, and took his penalty confidently, while 20-year-old Neto once again highlighted why he is one of the brightest prospects in football with his picture-book goal.