The 25-year-old, who suffered the setback in training on Tuesday morning in Kharkiv, is expected to be out for up to five weeks.
It’s another blow for Pep Guardiola, who is now down to one senior central defender after Stones joined Aymeric Laporte on the sidelines.
However, the boss took a positive stance during his pre-match press conference, saying it’s this kind of challenge and tactical conundrum that excites him.
“John Stones was injured this morning," he said. "He will be out for a month - 4, 5 weeks. The Problem is muscular.
“It’s a big challenge for me as a manager - it’s an incredible challenge with just one central defender, Nico [Otamendi].
“But I believe a lot in the spirit, the commitment to step forward and solve this problem.
"Fernandinho, and maybe Eric [Garcia] and Taylor [Harwood-Bellis] will come forward for the next few months.
“What we will not do is complain they are not able to play. We have 11 players on the pitch and we make an extra effort. I like this challenge.”
It seems likely Fernandinho, one of the world’s premium central-midfielders, will now be pressed into emergency action at centre-half.
The 34-year-old has played there on occasion under Guardiola, but is far from a specialist in that role.
But Guardiola does not foresee a problem with the Brazilian moving back into the defence - and the boss has challenged his squad to step up and be counted during a period of adversity.
“No problems,” Guardiola said. “It’s a challenge. Football is not how you handle good situations, but how you handle bad ones.
“We won seven titles and no one gave is anything, we did it ourselves.
“I am ready for the challenge; I like this situation.”