Scott Wootton's goal early in the first-half was enough to settle the game, although the Potters will be ruing a number of chances that went astray.
City's youngsters would have been keen to impress with some distinguished guests in attendance including Premier League Chief Executive Richard Scudamore and England Under 19s manager Noel Blake to cast their eyes over the Under 21 League's inauguration.
Both sides made use of the rule that allows three over 23 players and one senior goalkeeper in the squad - Carlo Nash, Michael Tonge, Diego Arismendi and Mamady Sidibe all started for the Potters, while Darren Fletcher continued his recuperation from his long-term lay-off for United.
As expected, the match started off at a high tempo and it was an action-packed opening ten minutes.
Stoke went very close to breaking the deadlock when Andy Musungu's square ball found Abu Kargbo, but the crossbar came to the visitors' rescue.
United soon took command and edged ahead on eight minutes.
Wootton showed no hesitation in bombing forward from full-back, and it was his looping shot that evaded Nash and went in off the post after good work from Ryan Tunnicliffe.
Three minutes later, they nearly doubled their lead - Joshua King cut in from the left flank, and his curling shot forced a smart save from the Stoke 'keeper.
The quality of the Red Devils' line-up was showing, but Stoke rallied and started to have some regular possession of their own.
On 18 minutes though, King robbed Arismendi and found Davide Petrucci advancing in the right channel, but City skipper Ben Heneghan was on hand to block his shot on the line.
It was real backs-to-the-wall work for City, but they had an opportunity of their own 25 minutes in when Michael Clarkson's pinpoint cross found Kargbo, and his header forced an impressive reaction stop from Sam Johnstone.
It was productive spell for the Potters, and Musungu forced another save from the United 'keeper six minutes later after his drilled effort from 18 yards.
The tricky winger had an even better chance eight minutes before half-time, however - Sidibe's blocked shot fell to him on the penalty spot, but he dragged his left-footed shot wide.
Unfortunately for Stoke, Sidibe was forced off injured moments later, with Jordan Richardson replacing him as Dave Kevan's side switched to a 4-5-1.
Half-time came and City would have been content with their display after weathering the early storm, but would been disappointed not to have drawn level.
Musungu remained the Potters' main threat, and only four minutes into the second period he found space on the edge of the area but again missed the target.
Two minutes later and the ball was in the net for Stoke. Musungu slipped a superb pass through to Kargbo who rounded the 'keeper and scored - only for the linesman to raise his flag for offside, although later replays showed the German forward had time his run well.
Stoke were the better side but blew another chance when Richardson's intercepted shot fell to Arismendi, but his shot lacked composure and cleared the bar.
A minute later and United should have doubled their lead - Wootton's cross from the right was perfect for the unmarked King, yet Nash did well to smother the header.
The marauding Wootton then had a chance of his own on 66 minutes when he was played in by Jesse Lingard, but once again City's stopper was on hand to turn the shot around the post.
With fifteen minutes left on the clock, Kargbo found Richardson on the edge of the area for the Potters yet his shot succeeded only in curling wide and you began to consider whether the luck was with the visitors.
United were proving resolute at the back, though to Stoke's credit the fitness work they had done in pre-season was clearly paying off as they showed tremendous energy in the closing stages.
It wasn't enough to earn an equaliser though, and it was United who got their season off to the best possible start with three points.
Kevan said afterwards: "They showed they were ready today. I can't have any complaints about our performance, we could have been a little more clinical with our finishing.
"We were disappointed to concede the goal in the manner we did - it was a bit of a fortunate strike from the lad.
"We'll take a lot of confidence into the Aston Villa game, but it will be another really good test for us and hopefully one we'll be ready for."
On Sidibe's injury, he added: "He had an attempt on goal. He felt something around his groin region, although it's too early to say how serious it is."
City's Under 18s were also in action, and they came from behind to beat Manchester United 2-1 thanks to goals from Derice Richards and James Alabi.
Stoke City: Nash; Glasgow, Heneghan (c), Jordan Keane, Clarkson; Hall (Thomas 74), Tonge, Arismendi, Musungu; Kargbo, Sidibe (Richardson 39). Subs not used: Bachmann, Dawson, Rigg.
Manchester United: Johnstone; Wootton, Michael Keane, Thorpe, Blackett; Cole, Fletcher, Tunnicliffe, Petrucci (Fornasier 68), Lingard (Veseli 90); King (Lawrence 90). Subs not used: Gollini, Januzi.