Carlos Mendes Gomes made a welcome return to action as Wanderers fell to a narrow defeat in the Central League.
Mendes Gomes played the first half at Lostock as he stepped up his comeback from the Achilles tendon injury he suffered at the end of February.
The forward made a lively start as he edged towards a first-team return but couldn't prevent Stoke leaving with the points after Conor Carty - another on the comeback trail - saw a late penalty saved for the Whites.
In a game of few chances, Stoke, with a couple of first-teamers in their starting XI, took the lead inside the first 20 minutes with what turned out to be the winner.
B Team Boss Andy Taylor: "It was two similar systems against each other, with a lot of man-to-man battles all over the pitch. I think at times both teams cancelled each other out. We struggled to create too much, they struggled to create too much. Obviously the goal from our point of view was an avoidable one.
"But it was good to see Carlos back in the first half and come through unscathed. Conor has been out a long, long time. He's building up his minutes all the time and getting fitter and stronger but obviously he's still going to be very rusty."
The visitors started brightly through Darius Lipsiuc who got on the end of a through-ball but the Republic of Ireland youth international fired his shot straight down the throat of Luke Hutchinson on 11 minutes.
Lipsiuc then fired wide but a clearance from Hutchinson then fell to Sol Sidibe who struck from outside the area to claim the only goal of the game.
Luke Matheson had threatened on the break for Wanderers but Wiktor Gromek came close to scoring a stunning goal to double Stoke's lead. An outside of the foot attempt from 25 yards crashed off the outside of the post and out for a goal kick.
Stoke created a couple of further opportunities after the break when Gromek and Lipsiuc both fired wide before Wanderers looked to reply through half-time substitute Carty.
The striker - working his way back from a knee injury sustained on loan at Doncaster Rovers at the end of January - threatened with an effort from range but with too much on it, the ball went over the bar on 68 minutes.
Carty was involved once more nine minutes later when he was brought down in the area . The youngster dusted himself down and stepped up to take the spot-kick but Jack Bonham guessed correctly and kept the effort out by diving to his left and parrying the ball away.
Pijus Otegbayo had the final chance of the game but was denied a goal from outside of the area thanks to a fantastic diving save from Hutchinson who kept the deficit at one in Wanderers' final game of the year.
Wanderers: Hutchinson, Toole, Hogan, Weston, Matheson, Halford (C) (66' Leigh), Irwin, Westwood (81' Nuttall), Eze (46' Carty), Mendes Gomes (46' Bryan), Isong (66' Abimbola).
Stoke City: Bonham, Agina, Dixon, Anderson, Otegbayo, Gromek, Lipsiuc, Sidibe, Chibueze, Tezgal, Griffiths. Substitutes Used: Jeffers, Kelly, Gyimah, Willox
Referee: Nathanael Cox
Images: Ben Livingstone