He said: "There was contact. Maybe the referee didn't feel there was enough contact.
"He shouldn't have booked him from my point of view.
"After the game, he can watch a replay and it's easy to make that decision."
The European champions have been denied several penalty claims in recent weeks but Di Matteo ruled out making a formal complaint to referees' chief Mike Riley.
Chelsea looked set for a fourth straight match without a win before Ashley Cole spared the blushes of their £130million attack with his first goal since May 2010.
But Di Matteo said: "I thought it was just a question of time before we scored.
"Obviously, when it comes towards the last 20 minutes, time is running out.
"But when you play against Stoke, it's always so hard to break them down and they defend with so many men and they're very well-drilled as well."
Di Matteo admitted it would take time for Eden Hazard, Oscar and Juan Mata to click after handing the £80million trio their first start together.
They failed to get Fernando Torres scoring but Di Matteo said of the £50million man, who flopped again: "He's in a very good mood because he's in a team that's at the top of the league."
Di Matteo also revealed Daniel Sturridge could be fit for next weekend's trip to Arsenal, when John Terry and Frank Lampard are also expected to return after starting Saturday's game on the bench.
The Italian insisted the pair had been omitted to avoid burnout later in the season, scoffing at suggestions it had anything to do with Roman Abramovich - who watched Saturday's game - visiting Chelsea's training ground on Thursday after the club blew a 2-0 lead to draw against Juventus.
"Come on, seriously now? Seriously?" he said, refusing to rule out picking Terry for Tuesday's Capital One Cup clash with Wolves.
That is despite it being understood his captain's Football Association hearing over the Anton Ferdinand saga is set to begin on Monday.
"Let's see what the outcome is first," he said.
Di Matteo also played the wait-and-see game over Cole's contract talks, with the England left-back's current deal due to expire next summer.
He said: "My recommendation, of course, to the club is to make him stay here as long as they can.
"They'll find a solution, I'm sure, because both parties are happy to talk."