Villa were unable to hold on to what would have been a creditable point at the Britannia as Stoke scuffed in a late winner.
The newly promoted Potters, backed by a capacity crowd, went ahead twice only to be pegged back by goals from John Carew and Martin Laursen.
But, Mamady Sidibe's injury time header left Villa with no right of reply and gave Tony Pulis' men their first Premiership points.
The Claret and Blue knew they were in for a scrap, but they couldn't have predicted the influence that referee Mark Halsey would have in the first half.
He waved away a strong penalty appeal from Gabby Agbonlahor and then proceeded to award the hosts a spot kick at the other end.
However soft Stoke's penalty claim was, it mattered not one iota to Liam Lawrence, who put the ball beyond a despairing Brad Friedel.
Pulis obviously warned his side not to rest on their laurels and they continued to pressure Villa until the break.
Martin O'Neill left the touchline with an anger strewn expression etched on his face and quickly followed Halsey down the tunnel.
Pedestal
But the second half was better for Villa and John Carew levelled after a neat interchange with Ashley Young.
Once again, though, they failed to hold parity for long as Ricardo Fuller scored with a neat finish.
The towering figure of Martin Laursen looked like he had rescued a point when he scored from close range.
But, it wasn't to be, as Stoke's Boltonesc tactics paid off, with Mali international Sidibe putting the ball past Friedel from a long Rory Delap throw in.
Inevitably, it seems Stoke will use a physical approach in their fight for survival this season and if Villa are anything to go by it might just work.
The Claret and Blue will be ruing the result as it was a game they would have, and should have expected to win.
With Liverpool set to come calling next weekend, it doesn't get any easier and points away from home against bottom half sides will be crucial.
But after such a fine win against Man City, the Stoke defeat will make the players realise they can't sit comfortably on their pedestal.
They must react and react quick because the fans will expect better in the big grudge match against Rafa Benitez and his boys.