David Jones brilliantly flicked up a free-kick to volley into the top corner on 36 minutes before Steven Fletcher bundled in a debut goal to double the advantage.
The Potters hauled themselves back into the match after 55 minutes when Matthew Etherington picked out Abdoulaye Faye from a corner and the Senegal defender powered a header past Marcus Hahnemann.
Stoke's misery was compounded by the loss of record signing Kenwyne Jones through injury after just 14 minutes.