The Group E contest at the Clayton Wood Training Ground saw the Potters earn victory on home soil to secure the points.
The Reds enjoyed two of the best opening chances to the match as Finn Inglethorpe saw a shot deflected just wide after strong work from Charlie Huth on the right.
The striker again tested the home goalkeeper after he picked up the ball outside the box to turn and shoot, though stopper Oscar Hatton was equal to the opportunity.
However, it was Stoke who took the lead just after 20 minutes as a ball over the top of the Liverpool defence allowed Louie Bradbury to finish well.
The Reds almost responded through Erik Farkas as he curled an effort inches wide of the post after Haydn Murray-Holme and AJ Yeguo had combined in the build-up.
Stoke, though, doubled their advantage with Bradbury’s through ball finding Noah Pinder, who rounded goalkeeper Matty Wright to score.
Ahead of the half-time interval, Liverpool did cut the deficit in half, with Inglethorpe getting on the scoresheet via a header.
The forward was on the end of a cross from Isaiah Garin as he delivered from the byline to find his teammate.
After the half-time break, it was Stoke who quickly added to the scoreline through Pinder during a swift counter forward as the hosts broke down the right side to deliver.
The Potters then restored their two-goal advantage by adding another through Bradbury as Pinder turned provider again after winning the ball high up the pitch.
Huth then saw an opening from in close blocked on the line by Stoke after a dangerous cross from Yeguo opened up the chance.
Substitute Joe Dixon also forced Hatton into a brilliant save from a corner ball to ensure the Potters’ healthy lead remained.
However, Stoke again had the final say of the afternoon with Liverpool pushing forward, with substitute Jahdell Holgate scoring on a rebound following a Wright save.
Liverpool: Wright, Garin, Owen (Powney Wain, 60), Conde (Dixon, 46), Clarke, Murray-Holme, Huth, Hickman (Eden, 65), Inglethorpe (Coxon, 73), Farkas, Yeguo.
Unused sub: Dooley.
