First half strikes from Adam Thomas and Robbie Parry, as well as a third from Tomi Adeloye during the closing stages of the game were enough to claim the win for the young Potters.
The fixture was the side's third of pre-season following matches against Bognor Regis Town and Brighton and Hove Albion as they continue to build up their fitness ahead of the new campaign.
After a rather drab opening half hour it took until the 32nd minute before either team fashioned a real opening and it proved to be profitable for Glyn Hodges' team when the ball was played into the path of Thomas and the former Everton winger coolly fired home into the bottom corner from 10 yards.
It seemed to spark City into life and the visiting supporters didn't have to wait too much longer to cheer another Potters goal as midfielder Robbie Parry superbly fired a 25-yard effort into the top corner of the net four minutes later.
The Potters finished the half strongly and moments after the interval Nathan Ricketts-Hopkinson may have been disappointed not to have grabbed himself a goal after being unable to apply a powerful touch to a swift counter when well placed inside the box.
The home side failed to trouble Dale Eve in the City goal with long range efforts from Aaron Carter and Neville Thompson as Newcastle looked for a way back into the game before the hour mark.
A host of substitutions on 60 minutes from Hodges saw Peter Skapetis lead the Potters attack and the Australian Under-23 international had two good opportunities to add to Stoke's lead but his close range effort was turned behind by Alcock, before the stopper expertly saved what looked like a certain goal on the line moments later.
Town never gave up hope of finding a route back into the game and they pulled a goal back on 78 minutes as Thompson headed in Elliot Osbourne's left-wing cross from six yards.
It was City however who finished the stronger and Adeloye grabbed his second goal of pre-season with a simple tap in seven minutes from time, before seeing a 25-yard effort well saved by Alcock in the game's final piece of action.
Stoke City: Eve, Wheeler (Strong 60), Barber (Cook 60), Ward (Shenton 60), Coulson (Grant 60), Watkins (Monlouis 60), Thomas (Adeloye 60), Parry (Lecygne 60), Alabi (Skapetis 60), Jerome (Ricketts-Hopkinson 45), Taylor (Nardiello 60).
Meanwhile, John Perkins' Under-18s secured a 2-1 win against Birmingham City earlier in the day at the Clayton Wood Training Ground.
A first half own goal from the visitors was added to be a tidy finish from midfielder Kelvin Douglas after the interval, before the Blues set up a tense finale with an 18-yard effort which beat the outstretched arm of Chris Marques in the City goal.