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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.
"It's a bitter disappointment given the current situation," Neuer told the club's official website.
