Club-record signing Kenwyne Jones had earlier marked his home debut with an equaliser to Stewart Downing's 35th-minute header on an emotional night for the Potters, who collected their first points of the campaign.
Manager Tony Pulis missed the first half after the death of his mother earlier in the day but returned after the interval, while new Villa boss Gerard Houllier was absent due to his commitments with the French Football Federation.
Houllier hopes to be in the dug-out for Saturday's game against Bolton but caretaker Kevin McDonald has done an admirable job in trying circumstances since Martin O'Neill walked out on the eve of the season.
Monday night Premier League football has not been kind to Stoke in the past, having failed to score on both previous occasions when they played.
However, the opposite had been true for Villa heading into tonight's match, and they had lost only one of their last 13 top-flight matches at the start of the week.
It seemed that statistic was going to be tested early on as Stoke dominated but could not make their pressure pay.
By contrast, once Villa scored it was all one-way traffic until half-time.
A breakneck pace suited Stoke's high-energy game and they had a number of half-chances, with Robert Huth's shot deflecting off Stephen Warnock to present Brad Friedel with a comfortable save.
Jones had an impressive first appearance in front of his own fans and looked a constant threat to Villa, forcing Friedel into an 11th-minute save having been put through by the deadline-day arrival from Portsmouth, Marc Wilson.
Having headed Matt Etherington's right-wing corner wide, Jones then produced a brilliant piece of skill to chest down Thomas Sorensen's clearance and hit a swerving 25-yard left-footed volley on the turn which the Villa goalkeeper had to parry away.
Villa midfielder Marc Albrighton's received a talking-to for appearing to swipe Dean Whitehead around the head and from that point until the break the visitors took control.
Gabriel Agbonlahor's 35th-minute curling left-footed cross to the far post caught Huth in two minds and he chose the wrong option as he stepped towards the ball only to see it sail over him.
Downing timed his run and dive to perfection, planting a low curling header past Sorensen and in off the right post.
Stoke felt they had justifiable claims for a penalty moments later when James Collins seemed to handle under pressure from Jones but Probert waved away appeals.
Ashley Young should then have put Villa further ahead only to head wide from close range from Agbonlahor's cross when it looked easier to score.
As the half drew to a close Sorensen was the busier goalkeeper, batting away James Collins' close-range drive and then clawing out another Downing effort.
Pulis made an emotional appearance for the second half to take up his position in the technical area, immediately giving the crowd and his team a lift.
Five minutes after the restart Friedel kept out Jones' header from Etherington's free-kick, with the goalkeeper then pawing away Rory Delap's long throw under pressure from the Trinidad and Tobago international as Etherington's follow-up was blocked.
Stoke were back in the ascendancy but their hard work was almost undone by a misunderstanding between Ryan Shawcross and Sorensen which resulted in the goalkeeper blasting the ball at Nigel Reo-Coker and back over his own crossbar.
However their endeavour finally paid off in the 80th minute when Ricardo Fuller combined with Etherington on the left of the penalty area and the winger sent over the ideal cross for Jones to head home.
The former Sunderland striker pulled out his trademark somersault celebration but despite the equaliser Stoke still had to be alert and Shawcross deflected Reo-Coker's shot behind in the last five minutes.
Substitute Fuller's response was to twist his way into the area before forcing a save out of Friedel.
Deep into three minutes of injury-time Jermaine Pennant's free-kick dropped to Etherington and his shot was deflected in by Huth to secure the home side's first win of the season.