Shaqiri was substituted at half-time as Bayern suffered a 1-0 defeat at Augsburg on Saturday, a result which ended a 53-game unbeaten run in the Bundesliga for Pep Guardiola's men.
The Bavarian club have now confirmed that Shaqiri will be unavailable for Wednesday's UEFA Champions League quarter-final second leg with Manchester United after tearing a muscle in his right thigh.
The Switzerland international's absence further weakens Bayern's midfield ahead of the crucial clash with United.
Bastian Schweinsteiger and Javi Martinez are both suspended for the tie, while Thiago Alcantara is out with a knee injury.
Bayern have the advantage of an away goal following a 1-1 draw in the first leg, but goalkeeper Manuel Neuer concedes that their injury problems are concerning.
"It's a bitter disappointment given the current situation," Neuer told the club's official website.
