The Switzerland international faces what could be a lengthy spell on the sidelines with a muscular problem.
The Switzerland international suffered a torn thigh muscle and was substituted at halftime 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 has now confirmed Shaqiri will be unavailable for the second leg of the quarterfinal tie.
"The midfielder reported to Dr. Hans-Wilhelm Muller-Wohlfahrt’s clinic in the evening, where the FCB Chief Medical Officer diagnosed a badly torn muscle in the right thigh. Shaqiri will be sidelined until further notice," a statement on the club's official website reads.
The Switzerland international's absence further weakens Bayern ahead of the crucial clash with United as Bastian Schweinsteiger and Javi Martinez are both suspended for the tie. Thiago Alcantara, Diego Contento, Tom Starke, Lukas Raeder and Holger Badstuber are also unavailable.