The European champions have confirmed that the 23-year-old full-back is facing an unspecified spell on the sidelines with ankle ligament damage
The 23-year-old has featured on only nine occasions in the Bundesliga this season but had been expected to start at the SGL Arena, given coach Pep Guardiola is likely to rotate his squad this weekend with Wednesday's Champions League quarter-final second leg against Manchester United in mind.
However, Contento is now set for a spell on the sidelines, though Bayern did not specify how long the Munich native will be out of action for.
"Pep Guardiola will be without Diego Contento for Augsburg due to a ligament injury in his left ankle - get well soon," Bayern posted on their official Twitter account.
Contento has risen through the ranks at Bayern, but has largely played second fiddle to the likes of captain Philipp Lahm and regular left-back David Alaba.