Musiala was forced to withdraw from the Germany squad after suffering a minor muscle tear before the 1-1 draw with the Netherlands in Amsterdam during September's international break.
The 23-year-old has now returned to the training pitch for individual work as he builds up his fitness.
"Musiala worked with fitness coach Simon Martinello prior to team training, doing drills focused on changes of direction and enjoying some time with the ball at his feet," Bayern said.
The attacking midfielder is yet to receive a confirmed return date, with Bayern still expected to be cautious over his comeback.
Musiala is likely to miss Saturday's Bundesliga meeting with Augsburg and Tuesday's Champions League clash with Viking, but his return to ball work represents another positive step in his rehabilitation.
