Robben picked up a hamstring problem against Hertha Berlin last week and consequently missed the 2-1 Bundesliga win over Hoffenheim on Saturday.
The 29-year-old was initially expected to be match fit again in time for Tuesday's Group D clash against Plzen, but Bayern have now announced on their official website that Robben will remain in Munich to continue working on an individual training programme.
The winger has been a key figure for Bayern so far this season, scoring eight goals in 15 appearances in all competitions.
Bayern currently sit atop of their Champions League section with nine points from three games and will qualify for the knockout stages with a win over Plzen.