Stoke forged into a 2-0 lead with goals after 33 and 59 minutes before Ruben Lameiras pulled a goal back with a superbly-flighted free-kick after 69 minutes.
There were chances either end after that but it stayed 2-1 at Stoke's training ground.
"In many ways I was quite pleased because after the game against Barcelona on Thursday, it was an opportunity to make a couple of changes," said coach Alex Inglethorpe.
"We've said from day one it's not about winning, it's about developing players so with that in mind, I was really pleased.
"We started two Under-16s players in Josh Onomah and Channing Campbell-Young and at Stoke, it was always going to be a challenge.
"It was a fantastic opportunity to see how the players coped with the physical side of it and for the first half-hour, I thought we were excellent.
"We were content to play two-for-two at the back and didn't look for more protection, we wanted to see how young Channing and Connor (Ogilvie) would cope against two physically imposing players and they did really well. They will benefit from that experience.
"Overall, I think we deserved our goal but didn't deserve to win the game. Having said that, the younger players will take invaluable experience from it."
Spurs U18s: McGee, Bush (Miller, 60), Campbell-Young, Ogilvie, Smith (Gardiner, 86), Lameiras, Onomah (Vincent-Young, 77), Winks, D McQueen, Akindayini, Coulthirst.