American international Brek Shea bagged himself a first half brace against the Welsh outfit with Development Squad forward Peter Skapetis also netting before the interval to complete the win.
City could have added further to the scoreline in the second half but home 'keeper Mike Askew stood resolute to protect his goal from further damage.
Former Welsh international winger Glyn Hodges named a strong starting line-up with Andy Wilkinson, Ryan Shotton, Jamie Ness and Shea all fielded against the Lilywhites and it was their experience which helped the Potters to control proceedings from start to finish.
City had made a bright opening against the Welsh Premier side when Jack Nardiello looped over a header after just 40 seconds before Shea forced Askew into a smart save from distance.
The 24-year-old was looking lively in an attacking position for the Potters and after seeing Skapetis plant a tame header into the keeper's gloves, the winger put City ahead on 17 minutes when he tapped in from close range following a low cross from the right.
Hodges' side were passing the ball around with real freedom and with their next attack they made it two when Shea latched onto Skapetis' throughball to coolly fire home from 10 yards and past the onrushing keeper.
Stoke looked like they were about to score with every foray forward as Eddy Lecygne and Nardiello both went close with efforts, before City were finally troubled in the 32nd minute but Wilkinson was on hand to head away at the far post when under heavy pressure from Aaron Bowen.
Nardiello, who was capped at youth level by Wales, looked lively on home soil and it was his pass which allowed Skapetis to make it three minutes before the break when the forward powerfully drove a low shot inside Askew's near post.
The Australian Under-23 international continued to cause problems in the second half and he would have scored the Potters' fourth with a clever near post flick but for a superb reaction save from the Rhyl keeper which denied him.
City never lost their stranglehold on the game and Ness was next to try his luck with two 20-yard efforts which flew wide before Skapetis stung the palms of Askew from distance.
Left back Elliot Wheeler then fired into the keeper's stomach with a long range effort, whilst Shea went narrowly close to netting a hat-trick goal when he worked himself some space on the edge-of-the-area and curled a left-footed effort just wide of the far post.
Nardiello had City's final opportunity in the dying moments when he fired off target from just inside the area but it wasn't to matter as the Potters XI rounded off an unbeaten pre-season with a win.
Stoke City: Kurasik, Wilkinson, Shotton, Watkins, Wheeler, Skapetis, Ness, Trialist, Lecygne, Shea, Nardiello
Meanwhile, Stoke City's Under-18s secured a 2-1 victory against Sheffield Wednesday at Clayton Wood earlier in the day.
Goals from midfielder Oli Roberts and German forward Yusuf Coban put the young Potters into a commanding lead before the Owls netted a late consolation goal.