Shaqiri was one of the prime contenders to replace the already injured Franck Ribery but tore his right quad during the 4-0 win over Freiburg on Saturday.
The Swiss winger had played himself right into contention for the first-leg against the Gunners on Wednesday night by scoring two goals in a win that put Pep Guardiola's men 19 points clear at the top of the table.
Bayern will now likely start with Arjen Robben and Mario Gotze on the wings at the Emirates.
Shaqiri meanwhile faces an estimated two weeks on the sidelines.
- Sports & Recreation
- Franck Ribery
- Arjen Robben