Stones has revelled in a new hybrid role where he moves between right back and into central midfield when City have the ball.
The defender has been asked to play in the position in previous seasons, but it has become a more regular feature of City’s set-up in recent weeks.
But Guardiola says the role requires complete concentration ahead of Saturday’s Premier League clash with Southampton at 17:30 (UK).
“Our shape was completely different [in the past] and that’s why maybe he struggled a little bit more and now he knows, he practiced more, he knows more our routine is a little bit better and that’s why he can use it better,” the boss said.
“At the same time, it’s a new position for him and he has to be able all the time to concentrate more than when you play as a central defender or other positions.
“When you see the game from behind it’s completely different to when you play in the middle and are surrounded. Some movement and patterns are a little bit more difficult that’s why I appreciate a lot what he has done.”
Guardiola has always wanted his sides to play out from the back which is why Stones has been such an important part of our success in recent seasons.
“We saw some specific things [in John] with the ball, especially in the build-up,” he added. “We were happy to have him but all that he has achieved here and with the national team belongs to him.
“We know the qualities, who is fast, not fast, who has the ability to make the receptions, their body shapes and the quality of the pass, the vision, anticipate what happens, one against one - you discover them. You see them day-by-day, after training, game-after-game and you realise it.”
Academy player Rico Lewis has also taken on the role after breaking into the first team this season and making 18 appearances already.
Guardiola says the 18-year-old is perfect for the role after playing as full-back and in midfield during his time coming through the youth teams.
“Rico is a perfect position for that,” he said. “He was before a holding midfielder and now with the right back, he can play both.
“As much as the people behind go forward, it’s more difficult. The players who start to play forward go backwards, it’s easier. So that’s why you always have to think about it.”