The club's official Twitter account announced the England international had to be substituted early due to a knock:
After the match, City manager Pep Guardiola told reporters that Stones' injury is "just a kick."
After joining City from Everton in the summer, this injury is a minor setback for the player.
Under the guidance of former Everton boss Roberto Martinez, the youngster failed to get the balance right between defending and ball-playing. That's something he'll be looking to improve as he develops in his career, with Guardiola an ideal mentor.
Stones has struggled for consistency in his first season at the Etihad Stadium, putting in a few excellent performances to go with a handful of poor ones. He remains one of City's top options at the position, however.
For club and country, Stones usually offers an assurance that is scarcely seen when it comes to English defenders. He's confident in his passing and at ease bringing the ball out from the back. There have been signs of a burgeoning authority from the player at times, too, as the 22-year-old can tackle, challenge in the air and read danger well when he's focused.
City have depth at centre-back with the likes of Nicolas Otamendi to call upon, while Aleksandar Kolarov also slotted into the role earlier in the campaign and replaced the youngster on Monday.