The R's have sunk back to the bottom of the table following a contest in which they were the better side for long periods, only to be undone by Charlie Adam's 52nd-minute strike.
Adel Taarabt wastefully chipped over for the visitors when presented with a good chance just before the interval and was unable to convert further opportunities after Adam's goal while Potters goalkeeper Asmir Begovic did well to keep out an Esteban Granero effort.
"We have played games this year that we should never have lost," said Pulis, whose team registered what was only their second win of the campaign and are up to 12th.
"He (Hughes) will be disappointed, with the chances they have created, that they haven't scored some goals. But you need to eke out results."