The Bosnia & Herzegovina international tore his hamstring in September and a "reaction to the injury" has ruled the centre-back out of the trip to Germany.
"He's come back into the team having been injured, you always want your top players fit, but he has had a reaction to the injury, so it's disappointing," Rodgers told Sky Sports News.
"We've had to get used to injuries, especially across our back line. Ideally, you want to have a set pair at the back, but we've had to constantly rejig the team. But whoever I put in there always does a great job."
Both Celtic and Bayern have three points from their opening two rounds of Champions League games heading into their two head-to-head clashes.