Robben, who has netted 19 goals this season, lasted just 16 minutes on his second-half come-back in the German Cup semi-final defeat by Borussia Dortmund on Tuesday after a month out with torn stomach muscles.
Bayern have already wrapped up the Bundesliga, but face Barcelona in the Champions League semi-final first leg next week.
And there was worse news for the Bundesliga champions, with Robert Lewandowski suffering a fracture to his nose and upper jaw in a clash with Dortmund goalkeeper Mitchell Langerak.
The club described the Poland striker's injury as "serious", but said further tests were needed to determine how long he would be out for.
Lewandowski said he hoped he would be fit for the away clash with Barca in a week's time.
"Its a few more days till the match at Camp Nou, i really hope i will be able to play!" he said on Twitter.
Bayern's attacking midfielder Thiago Alcantara is also facing a race to be fit to play against his former club Barcelona having come off with a knock to the leg.
The 24-year-old has only recently returned after more than a year out with back-to-back knee injuries.