The France international winger made his first appearance of the season on Saturday with a late cameo off the bench in Bayern's 2-0 win over Stuttgart, scoring his side's second goal.
However, the 31-year-old's comeback has stalled as he will miss the City clash on advice from the club's medical team.
There is some good news for Guardiola, though, with the return of Arjen Robben from a knee problem that saw him sit out training on Sunday.
"Arjen is here, but Franck is not with us," he said at a media conference on Tuesday ahead of Wednesday's Group E opener at the Allianz Arena.
"The physios told me after training that Franck needs to go to the doctor and they told me he can't play."
The Bundesliga champions are ready for the threat posed by Manuel Pellegrini's side and keen to avenge the 3-2 home defeat at the hands of City when the sides clashed in last season's Champions League.
"We have learned how good teams are," added Guardiola. "I have also learned if not everybody defends well, we have big problems.
"They [City] have so much quality that means we have to run a lot. They have for example Fernandinho, [David] Silva, [Samir] Nasri, [Sergio] Aguero, [Edin] Dzeko, and [Martin] Demichelis.
"All these players are absolutely great, extraordinary, and we have to be in the position to dominate the game and when we don't have the ball we have to run, run, run.
"The first game is important for the tone of the group. It's a tough group obviously."