The Potters were undone by two Englishmen, with former Hearts winger Andrew Driver and one-time Derby and West Brom wide-man Giles Barnes scoring for the home side.
Driver opened the scoring directly from a free-kick in the 11th minute, and Barnes slotted the second goal two minutes from the end at the BBVA Compass Stadium.
Despite the loss, manager Mark Hughes said he took plenty of positives from City's performance.
"It was a very worthwhile evening for us in terms of boosting the fitness levels of the lads, because I don't think they will play in these conditions again for a while," he told Stoke City Player.
"It was incredibly tough out there for them, especially given the fact that they had a session this morning too - but that is what pre-season is all about.
"It would have been nice to have picked up a win but the fundamentals are building up the levels of fitness and working on the things that we have been doing in training on a daily basis.
"I think the lads did well in many areas tonight, despite the result. They started to play the ball out from the back and I think we controlled the play for long periods."