Swiss boss Ottmar Hitzfeld sent Shaqiri back to Munich for Bayern club doctors to look at the problem, but those examinations have shown that he will be out for six to seven weeks.
The 22-year-old has admitted that he is bitterly disappointed with the news, but expects to recover quickly after suffering a similar injury in the past.
He told Bayern's official website: "It's a bitter diagnosis. I'm disappointed, but I'll try to get fit again as quickly as possible.
"I've had one of these tears before, on my left thigh, and I recovered from it quite quickly so I hope it will be the same again this time.
"It really is bad timing. I'd had a great week. I was in good form, and now this happens. It's a shame, but I'm looking ahead and I'll be back soon."
Bayern boss Pep Guardiola will be without the youngster until December, meaning that Shaqiri is unlikely to feature in the Bundesliga until 2014 due to the winter break.