Last weekend, Kompany was forced off at half time in the Manchester derby, while Stokes has been sidelined for a month with a hamstring problem.
However, while the pair will likely miss Saturday's meeting with Tottenham Hotspur, Guardiola is hopeful of having both players available over the Christmas period.
The 46-year-old told reporters: "[Kompany] is much better. He has a little problem. I don't know if tomorrow he will be fit but hopefully in the next days he will be ready.
"I think [Stones is] at week four and the doctor said between four and six. He will be ready in one or two weeks."
Earlier this week, Guardiola claimed that City would enter the January market for a new defender.