Danny Ings scored twice as the Saints climbed out of the bottom three at the home side’s expense.
The striker opened the scoring on 21 minutes and then bagged his second early in the second half, after Jack Stephens had increased the lead.
Jack Grealish gave Villa hope with a brilliant volley but it was too little, too late on another difficult day for Dean Smith’s team, who also lost John McGinn to injury early on.
The Scot had to be helped off the pitch and looked in severe pain after hurting his ankle with the match just eight minutes old.
It set the tone for a dire day for Villa, who now face being without one of their most influential players for an extended period.
Unquestionably, this season is now all about avoiding the drop and on this showing, it is fair to question whether Villa have the fight for the battle ahead?
They certainly showed nowhere near enough against the Saints, a team who have been scrapping near the foot of the table all season.
Uncertain in attack, messy in midfield and all over the place at the back, this was comfortably their poorest performance of the campaign, in the biggest match so far.
The good news for Villa is they will quickly get the chance to put things right when they host Norwich on Boxing Day, yet their performance will need to be far, far better.
Villa’s team featured two changes from the one beaten 2-0 at Sheffield United the previous weekend, both of which came in midfield with Conor Hourihane and Douglas Luiz replacing Henri Lansbury and Marvelous Nakamba.
Smith was forced into another change with the game just a few minutes old, though it was one he would never have wanted to make.
McGinn, fired up after not being awarded a free-kick when he was challenged by Stephens, flew in to win the ball back off Cedric Soares but his left foot was caught in the turf as he landed.
The Scot appeared to be in serious pain and after several minutes of treatment needed the assistance of Villa’s medical staff to leave the field.
Villa created the first big chance when Matt Targett’s low cross from the left ran to Anwar El Ghazi at the far post but his shot was saved by Alex McCarthy.
The warning signs at the back were already there for the hosts, however, with Long going close when he headed a Nathan Redmond cross over the bar.
It was a chance the Irishman should probably have scored and the same applied to Villa’s striker Wesley soon after, with the record buy sending an El Ghazi cross badly wide.
The breakthrough for the Saints came on 21 minutes. Redmond lobbed a ball over the top, with Long outpacing Bjorn Engels to race into the box. Though Heaton was able to save his shot, the keeper only succeeded in turning the ball into the path of Ings, who tapped home.
The visitors had further chances to extend their lead before Stephens bagged their second 10 minutes later.
Engels blocked a close range Long effort, while Heaton had to be alert to prevent Hause from netting an own goal when the defender turned an Ings header back towards the keeper at close range.
Yet there was nothing he could do to keep out Stephens’ header soon after, with the defender comfortably outjumping El Ghazi to glance home James Ward-Prowse’s corner.
Villa desperately needed a moment of inspiration and Frederic Guilbert almost supplied it with a drive McCarthy had to tip over the bar.
But six minutes into the second half the hole Villa were digging for themselves got even deeper as the Saints added a third.
Redmond’s cross from the left wing was headed straight to Nakamba but rather than clear the ball the midfielder tried to find Engels and only succeeded in teeing up Ings for his second of the match.
Villa looked a beaten team until Grealish gave them hope with 15 minutes remaining. A corner was cleared to the skipper on the edge of the box and after chesting the ball down he sent a superb volley over McCarthy and into the top corner.
But a grandstand finish never materialised, with the Saints seeing out the win in relative ease.
21 - GOAL Southampton lead. Shane Long outpaces Bjorn Engels and though Tom Heaton saves the shot, Danny Ings is there to tap in the rebound.
31 - GOAL Villa’s afternoon takes another turn for the worse as Jack Stephens glances home James Ward-Prowse’s corner.
51 - GOAL Villa slip further behind due to more dreadful defending. Marvelous Nakamba tries to play the ball back to Engels but only succeeds in teeing up Ings for his second and Southampton’s third.
75 - GOAL Jack Grealish reduces the deficit with a superb volley from the edge of the box.
Villa (4-3-3): Heaton, Guilbert, Engels, Hause, Targett, McGinn (Nakamba 8), Luiz, Hourihane (Kodjia 57), El Ghazi (Trezeguet 68), Wesley, Grealish Subs not used: Elmohamady, Konsa, Lansbury, Nyland (gk).
Southampton (4-4-2): McCarthy, Cedric, Stephens, Bednarek, Bertrand, Hojbjerg, Ward-Prowse, Armstrong (Romeu 76), Redmond, Ings (Adams 86), Long (Obafemi 82) Subs not used: Yoshida, Vestergaard, Boufal, Gunn (gk).