The 22-year-old scored Bayern’s equaliser before being replaced by Thomas Muller in the 54th minute with an apparent hamstring injury.
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Musiala went down before gesturing to the bench that he would like to be brought off, he then hobbled off the pitch with help from Bayern’s medical team.
Speaking to the press after the game, director Max Eberl emphatically ruled him out for their upcoming Champions League game with Inter Milan.
Eberl said: “Jamal Musiala’s injury unfortunately doesn’t look good. Missing Inter game next week? Yes”
Vincent Kompany’s side will be without eight first team players for the quarter-final thanks to an ongoing injury crisis.