Saints no doubt settled far more quickly due to the low turn out and the Vila fans turning on their side.
Both teams were at full strength but it was Gordon Strachan who came away with the points.
Rory Delap tried to get Southampton off to another early start but his effort in the first minute went well over.
Claus Lundekvam tried to add to his international goal at the weekend, but his shot from a corner kick dribbled wide of Enckleman's post.
Villa could well have had the opener as Dublin carved the Saints defence with a ball to Vassell. The England striker tried to put it over Niemi but also put it over the bar.
The chances continued for both sides as Anders Svensson curled a freekick around the Villa post and Hendrie shooting straight at Niemi having turned Delap.
Anders Svensson created another opportunity, surging through the heart of a retreating Villa defence. His powerful shot couldn't beat Enckleman though.
Despite Saints having much of the play, Villa managed to put the visitors under pressure in their own area. Only good covering by Bridge and Lundekvam prevented Vassell getting a shot in.
Villa created plenty of space down the right four minutes later. Dublin knocked back the resulting cross to the path of Gareth Barry who put the ball narrowly wide.
Fabrice Fernades continued to impress with his skill and passing. His long range effort was comfortably saved by Enckleman after 22 minutes, but it relieved some of the pressure on Southampton.
Unfortunately, Villa continued to create. Niemi managed to tip the ball round the post to prevent Vassell getting the opening goal after 38 minutes. Samuel hit well over from the corner.
Paul Jones may be the Welsh number one, but it's easy to see why Niemi is always in goal for the Saints.
Although Svensson managed to get in a free header from Bridge's cross just before the break, Enckleman got across to make a comfortable save. It was Saints putting Villa under pressure before half time. Saints had most of the better play in the opening period, and although Villa had the better chances, Saints were getting on top.
Saints trend of quick starts continued in the second period. Alpay pulled back Brett Ormerod as the on form striker burst into the box from the kick off. Enckleman made absolutely sure that Ormerod wouldn't get a shot on goal by clattering into him. The referee immediately awarded a penalty and although it was Alpay at fault, he sent Enckleman from the pitch.
James Beattie took a short run up for the penalty and shot past the substitute 'keeper although Postma came close to saving it.
If the Villa fans though things were bad before, the prospect of being a goal down with ten men turned even more against their team.
On fifty three minutes, Vassell chose to run at goal himself rather than pass wide to De la Cruz which was the better option. Vassell's shot trickled harmlessly wide.
Vassells next effort was much more powerful and it forced Niemi to tip it over the bar. Dublin's shot from the corner was deflected wide.
Saints then survived a goalmouth scramble. James Beattie sliced the air but could have easily put Dublin's effort into his own net as the ball went across the face of the Saints goal.
Having survived some Villa pressure, it was Saints turn to attack. Beattie made a good run into the box on sixty two minutes, but failed to take control of an excellent ball from Anders Svensson.
Five minutes later saw Ormerod put a free header over the bar from Beattie's cross. Beattie continued to create plenty of space for himself, just failing to get on the end of an Ormerod cross on 68 minutes.
With Saints missing chances with only a one goal lead, there was always the chance that Villa could come back into the game.
An excellent turn and shot from Hendrie forced Niemi to save low down as Villa increased the pressure once more.
Alpay was presented with a golden opportunity to level the score on 81 minutes.Alpay slipped behind the Saints defence as a Villa freekick came into the box. However, the ball stuck under his feet and before he could get a shot in, the Saints defence cleared.
Saints were now dropping further and further back against the teen men of Villa, inviting pressure. So often in the past Saints have conceded with around ten minutes to go and there were some nervous moments.
Hadji hit a powerful shot two minutes after Alpay's chance, but Niemi was always behind it.
A minute late Michael Svensson wrongly decided to leave the ball for Niemi forcing a bit of a panicked clearance between them.
Saints finally got forward again with five minutes to go, but Beattie's effort was deflected wide. Saints were now a little more comfortable at the back and were looking to catch Villa on the break.
Rory Delap put the ball into orbit with a long range effort which redefined the word "ambitious" on 88 minutes.
Villa put together a late attack but Hadji's effort was closer to the corner flag than the Saints goal.
Saints last attack was the closest to a goal since the beginning of the half. Beattie's effort from out wide on the left came off the Villa bar before heading out wide to the right.
Saints ended the game as deserved winners. Strachan's men had dominated large parts of the entertaining game and prevented Villa from creating too many clear cut chances. Having seen some truly dreadful Saints performances against Villa in recent years, I was very pleased with Saints approach and they can be proud of a job well done and another three points on the board.