Kompany, who has been plagued by injury and fitness issues over the past year, made his return to the City side for their 2-1 victory over Crystal Palace on Saturday but was substituted following a collision with goalkeeper Claudio Bravo.
It was initially assumed that the player was suffering from concussion as a result of the heavy impact between himself and Bravo, but Guardiola confirmed that an injury to his knee forced him to be withdrawn from the City squad travelling to Germany.
"Fortunately nothing happened with his head," Guardiola told a news conference ahead of Wednesday's Champions League Group C match at Borussia Monchengladbach.
"The real problem is the knee. He will be out for the next few weeks."
Asked whether Kompany would be included in City's squad for the knockout stages of the Champions League, Guardiola said: "Now is not the moment. First we have to qualify."Reuse content