City captain Kompany was thrust back into action on Saturday in what was his first competitive appearance since picking up a calf problem with Belgium in August.
The 31-year-old completed 90 minutes in the Premier League leaders' 2-0 win over Leicester, which was soured by Stones' hamstring injury,
The England centre-back is expected to be sidelined for four to six weeks and Guardiola suggested he will look for reinforcements in the January transfer window as he aims for precaution over Kompany. However, with City competing on multiple fronts, the defender may be forced into more games the his manager would prefer.
"We have to take care of him and we are trying to do that. He missed more than two and a half months because he played against Gibraltar when the score was 9-0," Guardiola told reporters.
"We have to be careful in terms of how many minutes, how he feels. We miss him [when he is injured].
"It is a risk to play him more and more, but now Stones is out, we have a real, real problem in that position.
"We are going to discuss [the situation in] January, we are going to think about it, but not just because John is [injured].
"To play in all the competitions, you need a bigger squad because the players do not have time for regeneration before the next game."