Shaqiri was injured in his country's 2-1 victory over Albania on Friday, a result that booked them a spot in next year's World Cup in Brazil.
"This diagnosis is very bitter," said the 22-year-old, who also scored in that game. "I am disappointed and I will try to get back as fast as possible.
"I had a similar injury in the left thigh and I recovered pretty quickly."
Shaqiri joins a growing list of injured team mates, including long-time absentee Holger Badstuber as well as Spaniards Thiago Alcantara and Javi Martinez.
Bastian Schweinsteiger only recently returned to action after ankle surgery while Mario Goetze also came back days ago following a lengthy injury break.
Last season's treble winners are top of the Bundesliga and have also kicked off their Champions League group stage with two wins in two games.