Kompany was making his first appearance of the season after having to miss Euro 2016, but he walked down the tunnel just before full time after he picked up another fitness problem.
However, Guardiola is hopeful that the injury issue is not a serious one after admitting that he had been impressed with the Belgian's display on his return to action.
The 45-year-old told reporters: "The doctors are speaking with him, but hopefully it is not a big, big problem. We're going to wait for the result.
"Once they scored the goal, after I said: 'What happened?'. They said that Vincent had gone to the locker room. Hopefully, it will not be a big problem. We will have to wait. If he's injured, he's injured. He cannot stay on the pitch."
"It's not easy after a long, long time without playing. Defensively, he was so strong - he played really good."
City secured a 2-1 victory at the Liberty Stadium to move through to a last-16 tie with neighbours Manchester United.