Substitute Matt Doherty was brought down by Pierre-Emile Hojbjerg with VAR supporting referee Peter Bankes' decision to award a penalty.
Jimenez made no mistake as he cancelled out Danny Ings' 53rd minute opener.
But it could have been a hat-trick for the Wolves forward had VAR not rightly ruled out two of his goals.
Jimenez was ruled to have handled the ball before netting in the 31st minute and Patrick Cutrone was offside in the build up to the second disallowed goal.
All three VAR decisions were correct at Molineux today but the communication of these decisions dramatically needs to improve, writes Rosie Swarbrick.
30,000 people in Wolves' ground were left confused after two Jimenez first half goals were chalked off.
Just 'No goal' flashed up on the big screen after he had hit the back of the net twice.
It would not be hard for the VAR announcement to add a few extra comments of explanation to keep the people paying their money in the ground informed.
All that needed to be said to clear up the first disallowed goal was simply confirming a handball by Jimenez and how hard is it to clarify offside for the second?
The decision to award the penalty was a much smoother process.
It was clear the referee had sent the decision upstairs and the penalty was then confirmed.
But VAR needs to be made clearer for the fans paying to watch at the stadium.
And one thing is clear, Wolves need to recruit in central defence this January.
Jesus Vallejo had another shaky performance having been sent on for the injured Ryan Bennett just 17 minutes into this clash.
He was given another chance to stake his claim for a regular starting spot but with Romain Saiss and Bennett injured it just leaves Wolves worryingly short in central defence.
And it appears from that 73 minutes that the kid from Real Madrid is just not up to Premier League standards.
It was his tame clearance that was batted back by Hojbjerg towards Ings.
Conor Coady missed the ball and Ings fired home - Vallejo was the weak link but his shakiness and low confidence rubbed off on the others.
Jimenez, though, would get his deserved goal, and Jota showed how key he is to this team with his late electric cameo on his return from a foot injury.
Wolves boss Nuno Espirito Santo made two changes from the side that beat Manchester City 2-0 earlier this month.
Romain Saiss failed to recover from the hamstring tweak that saw him limp off just 13 minutes into that clash at the Etihad.
Ryan Bennett came off the bench to replace him and takes his spot in the starting XI for the visit of Southampton.
Left-wing back Ruben Vinagre moved to the bench with Jonny Otto taking his spot on that flank.
Diogo Jota was fit enough to start on the bench as he ups his recovery from a foot injury.
Nuno stuck with the 3-5-2 formation and it was a bright start by Wolves.
Cutrone and Jimenez looked hungry and it was the Italian who nearly fed Moutinho to open the scoring.
He rolled the ball to the Portuguese midfielder at the top of the box but Moutinho's fierce strike just flew over the bar.
It looked like the Wolves players were enjoying their football with a number of delightful touches from the men in gold and black.
But they just could not find that killer touch in the box as crosses from Jonny and Traore were cleared by Southampton.
Wolves continued to pile the pressure on the wings.
And when Boly's cross from the left was cleared over to Traore, Wolves looked dangerous.
His looping cross fell to Cutrone but his acrobatic effort was easily collected by Gunn.
Up the other end Southampton sparked into life as Danny Ings sprinted through on goal.
The ex-Liverpool man left himself with too tight an angle and his strike was stopped by Patricio.
Wolves were rocked by a fresh injury blow in the 17th minute.
Bennett limped off with Vallejo taking his role on the right of the back three.
And that enforced re-shuffle at the back saw the momentum swing to Southampton's favour.
Ings wasted another golden opportunity as a set-piece fell into his path in the six-yard box but a gold and black shirt blocked his effort.
Hojbjerg curled the ball wide and high of Patricio's right stick as forward Nathan Redmond continued to be a thorn in Wolves' side.
But Wolves would be left cursing VAR at half-time with Jimenez seeing two goals chalked off.
The first saw the Wolves man use his arm to help bring the ball down before and then slide the ball past Gunn.
The assistant referee had flagged furiously to alert the referee who sent the decision to VAR.
It rightly ruled that Jimenez had handled the ball with the referee booking the Wolves man.
The second was less clear cut with the forward's goal ruled out after Cutrone was ruled to have been offside in the build-up.
The forward's leg was just ahead of play before he picked up the ball in the box and sent the ball fizzing towards Gunn.
Gunn could only turn the ball into the path of Jimenez but VAR would rescue the Saints as the goal was chalked off.
That left it goalless at the break with Nuno making another change sending on Matt Doherty for Ruben Neves.
Neves had picked up a knock in the first half after Ings clipped his heel and he was the man brought off as Nuno shifted formation to 3-4-3.
Doherty returned to the right flank to aid young central defender Vallejo as Wolves looked to tighten up on that right-wing.
Manchester City two-goal hero Traore moved up front to join Cutrone and Jimenez in a front three.
But Wolves were lucky in the opening stages of the new half.
Vallejo had looked shaky in the first half and he gave Ings a chance to open the scoring.
The centre-half tried to pass the ball across the box but found the Southampton forward instead of Coady.
But thankfully for Vallejo, Ings' radar was off and he fired the ball straight down Patricio's throat.
The visitors kept pressing Wolves and the defence creaked open.
Vallejo's looping clearance fell into the path of Hojbjerg in the middle of Wolves' half.
He nodded the ball hopefully forward with Ings sniffing.
Coady stepped forward to clear but missed the ball with Ings pouncing to sprint through on goal.
This time the forward made no mistake as he slid the ball past a helpless Patricio.
But Wolves soon fought back with substitute Doherty making his mark.
The wing-back sprinted into the box and tumbled to the ground after he was tripped by Hojbjerg.
Referee Peter Bankes pointed to the spot but the decision was sent upstairs to be clarified by VAR.
The foul though was a clear one and with the spot-kick confirmed Jimenez did the rest.
The striker coolly slotted the ball into the left corner in the 61st minute as Wolves drew level.
Wolves looked more likely to grab a winner after that equaliser with the introduction of Diogo Jota for Cutrone igniting that front three.
Jota's introduction gave more freedom to Traore with the duo linking up sublimely but despite chances for Jota and Traore as the half wore on Wolves could not find a second.
Patricio pulled off a sublime one-handed stop to tip James Ward-Prowse's set-piece away as Southampton piled on the pressure in the closing stages.
But Wolves would hold on to secure a draw on a day that will be remembered for VAR.
28 - Wolves think they have opened the scoring - but VAR intervenes! Jimenez gathers a sublime long ball from Boly, rounds Gunn, and slots home. The review concludes Jimenez controlled the ball with his hand, though. Yellow card.
43 - Jimenez is sure he has broken the deadlock this time for Wolves, but VAR says no once more! This close-range finish from the Mexican is disallowed because Cutrone's leg was offside in the build-up. Jimenez can't believe it.
53 - Goal. The Saints are in front. A horrendous attempt at a clearance from Vallejo is headed back towards the Wolves defence. Coady comes out to control the ball but misses it, allowing Ings to put it past Patricio. Such a soft goal to concede.
61 - GOOOOOALLLLLL! Jimenez finally has his name on the scoresheet! A mazy run from substitute Doherty sees him tripped in the box by Hojbjerg for a penalty, and Jimenez, with a stuttered run-up, smacks the ball into the bottom corner.
88 - Top save from Patricio. Boufal displays some fancy footwork as he ends up being tripped by Dendoncker. Ward-Prowse steps up for the free-kick and whips it towards the top corner, with Patricio showing great reflexes to keep it out.
Wolves (3-5-2): Patricio; Bennett (Vallejo, 18), Coady, Boly; Traore, Neves (Doherty, 46), Dendoncker, Moutinho, Otto; Jimenez, Cutrone (Jota, 62)
Subs: Ruddy (gk), Kilman, Vinagre, Gibbs-White
Goal: Jimenez (61)
Southampton (3-4-3): Gunn; Yoshida, Bednarek, Vestergaard; Valery (Boufal, 75), Romeu (Danso, 82), Hojbjerg, Bertrand; Ward-Prowse, Ings, Redmond
Subs: McCarthy (gk), Stevens, Armstrong, Long, Adams
Goal: Ings (53)
Referee: Peter Bankes (Merseyside)