Stones was absent for the 2-0 win at Old Trafford and was an unused substitute for the Champions League second leg against Tottenham Hotspur a week earlier.
The 24-year-old has been in and out of Guardiola’s side of late, with either Nicolas Otamendi or Vincent Kompany coming in alongside ever-present Aymeric Laporte.
Stones has featured in just three of City’s last 15 games in all competitions and Guardiola said on Friday his failure to nail down a place was simply down to rotation.
“The week before it was Danilo and the week before it was [Fabian] Delph, now [Delph] is injured again,” he said.
“It was our decision. Not fitness, it was a decision on what I saw. Nico was important in the last months and in the last few games he’s not involved.
“I like to involve everyone, that’s what I’m looking for. Sometimes we need one specific quality from our centre-half. That’s the reason why.”
Guardiola started Kompany at Old Trafford and revealed that his decision had been influenced by United’s counter-attacking and direct approach.
“When it’s a lot of long balls I prefer Nico and Vinny,” he said. “When there’s more of a gap, like Chelsea, Stones is an incredible player in those situations.
“When teams play high, I like to have Leroy [Sane], when they are deep David Silva in the pockets.
“It depends on the quality of the players and what I see in the training sessions, if they are happy, a bit more down.
“There are many reasons but it’s not the quality because I know them and I know that always they compete good.”
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