Stones, who has been struggling with injury all season, started at centre-back but was replaced by Kyle Walker at half-time.
Guardiola confirmed the England international had suffered a fresh setback when speaking after the game.
Asked if the decision to take Stones off was tactical or down to an injury, the City boss said: “I would say I'm not in the right moment to make tactical and creative changes."
John Stones suffered a new injury problem for Manchester City against Aston Villa
City’s crisis has seen them fall to nine defeats in 12 games but Guardiola is optimistic of turning the worst run of his storied career around.
“I have incredible trust in these guys, some of them have incredible pride and the desire to do it, and we have to, I have to find a way to sooner or later, step by step, come back,” he said.