The centre-back was substituted in the 68th minute of the Champions League fixture on Tuesday, during which an understrength Bayern scored a late penalty to grab a 1-1 draw at the Wanda Metropolitano.
Gimenez has since undergone a scan and while the LaLiga club confirmed a thigh issue, a potential return date has not been announced.
However, Spanish media have suggested the Uruguay international is unlikely to feature for Diego Simeone's side again during a busy December.
Atleti have Real Valladolid next at home in the league, followed by a huge derby fixture against neighbors Real Madrid on December 12.
Sandwiched in between those domestic games is a pivotal Champions League clash with Salzburg, as they must avoid defeat in Austria to seal their progression through to the knockout stages of the competition.
Gimenez has played seven games so far in the 2020-21 campaign, having missed the early stages due to a positive coronavirus test.
The 25-year-old has started four times in the league, all victories. Atletico have only conceded once in those fixtures, while he was also part of a defensive unit that shut out Lokomotiv Moscow in European action at the end of November.
If unavailable for the remainder of 2020, Gimenez will also miss the start of his club's Copa del Rey campaign, as well as the LaLiga trip to Real Sociedad, which is currently scheduled for December 22.