The striker’s fourth Premier League goal of the season came after Southampton skipper James Ward-Prowse saw a goal chalked off after a VAR check.
Play had earlier been halted for around 10 minutes in the first half after a drone flew into the stadium.
After Watkins had broken the deadlock, Emi Martinez preserved the points with a stoppage time save to deny Moussa Djenepo.
Villa had the better of the chances in a match low on quality but lacked the killer touch until Waktins provided it, heading home Douglas Luiz's free-kick.
For much of the afternoon, the story looked like being about another striker. This was a match which appeared to be crying out for Danny Ings, Villa’s top scorer sold to West Ham on Friday.
Watkins’ goal was a big one in that respect, though a key turning point came before when Ward-Prowse saw his opener ruled out after referee Michael Salisbury checked the monitor and decided Mohamed Elyounoussi had fouled Jacob Ramsey in the build-up.
Villa took advantage and have now won five out of seven Premier League matches under Unai Emery, including all three away from home.
Alex Moreno replaced the injured Lucas Digne at left-back in the one expected change yet Emery’s sudden paucity in attacking resources, following the sale of Ings, was highlighted by the presence of Viljami Sinisalo as one of two goalkeepers on the bench.
Leander Dendoncker and Matty Cash returned among the substitutes after suspension and injury respectively but Ludwig Augustinsson and Marvelous Nakamba were both absent. Jan Bednarek was unable to play against his parent club.
Ramsey was making his second start since returning from injury and almost created something from nothing when he chased his own flick into the box, home goalkeeper Gavin Bazunu just about beating the midfielder to the ball and getting enough on it for referee Salisbury to award a corner, rather than a penalty.
Villa were bossing possession in the early stages but mainly in defence and Southampton were happy for them to keep it there. When the visitors did try to move it quickly, Mohammed Salisu was in place to make a crucial intervention and prevent Douglas Luiz from sending Leon Bailey through on goal.
The Saints were offering little, yet gave their opponents a warning shot when Lycano’s cross was allowed to travel to the far post and Che Adams and Kyle Walker-Peters, both in offside positions, bundled it home.
Nearly half-an-hour had passed before either keeper was forced into a serious save. Emi Buendia burst out of midfield and found Bailey, who picked out Ramsey with his cross. The latter sent his shot too close to Bazunu, though it was still a more than decent save, with Bailey blazing the rebound over the bar.
Villa were pushing now and Ramsey saw appeals for a penalty waved away when he tumbled trying to turn Salisu in the box.
This was hardly a match full of drama. Yet the crowd were treated to an unusual incident late in the first half when the presence of a drone at the Chapel End of the stadium forced a stoppage of around 10 minutes.
Villa remained in the ascendency after the restart but when Moreno crossed in stoppage time, Bailey slipped just as he was about to shoot.
The Jamaica international squandered another opening in the first minute of the second half. Bazunu’s clearance went straight to Ramsey 25 yards out and he immediately teed up Bailey, who sent his shot straight at the grateful keeper.
An hour had passed before the hosts mustered a serious shot on target but when they did Martinez needed sharp reflexes to keep out Adam Armstrong’s low drive from Ward-Prowse's cross.
Moments later the latter thought he had broken the deadlock. Kyle Walker-Peters crossed from the right and Ward-Prowse's shot deflected off Konsa, over Martinez and into the net. But Villa were adamant Ramsey had been fouled by Mohamed Elyounoussi and after consulting the pitchside monitor, referee Salisbury agreed.
The home supporters were unimpressed and 13 minutes from time Villa rubbed salt in the wound. Luiz delivered a free-kick and Watkins arrived unmarked to head beyond Bazunu.
Southampton didn’t threaten an equaliser until stoppage time but when Djenepo cut in from the left, Martinez proved equal to the shot, palming it wide.
63 VAR Southampton think they have taken the lead when James Ward-Prowse's deflected free-kick beats Martinez but the goal is chalked out after a VAR check for a foul on Jacob Ramsey.
77 GOAL Ollie Watkins heads Villa in front from Douglas Luiz’s free-kick.
Southampton (4-2-3-1): Bazunu, Lycano, Caleta-Car (Djenepo 84), Salisu, Walker-Peters, Lavia (Mara 62), Diallo, Armstrong (Orsic 84), Ward-Prowse, Edozie (Perraud 62), Adams (Elyounoussi 62) Subs not used: Maitland-Niles, Aribo, Orsic, Djenepo, Caballero (gk).
Villa (4-4-2): Martinez, Young, Konsa, Mings, Moreno, Ramsey, Luiz, Kamara, Buendia (Coutinho 69), Bailey (Cash 81), Watkins Subs not used: Sanson, Cash, Chambers, Dendoncker, Revan, Young K, Sinisalo (gk), Olsen (gk).