The Greece international was injured during Dortmund's 0-0 draw with Union Berlin on October 17. He had only recently returned after collapsing in September because of what the club described as circulatory problems.
Karetsas took part in part of Thursday's training session, giving Dortmund hope that he could be available for the trip to Munich.
"He trained in part with the team today," Kovac said. "The plan is that if all is well tomorrow, he will train with the team and we will decide if he is ready to go to Munich or not."
Dortmund head into the match after reaching the third round of the German Cup with a dramatic 3-2 home victory over Werder Bremen on Tuesday.
Saturday's clash could have a significant impact on the Bundesliga title race, with both sides unbeaten and level on 17 points after seven matches. Bayern lead the standings on goal difference.
However, Dortmund have scored only 12 league goals, fewer than half of Bayern's 25, underlining the challenge facing Kovac's team against the defending champions.
"It is the Klassiker, and after a long time we can play a game having the same level of points," Kovac said.
"That makes the match more interesting, but it does not make it easier. Bayern are the gold standard, not only in Germany but in Europe."
Despite Bayern's impressive attacking form, Kovac believes Dortmund have an opportunity to make a statement if they deliver a strong performance.
"We may have a chance this time to turn the game in our favour but, as I said, it won't be easy," he added.