The 22-year-old, who was forced to miss training on Thursday and Friday with the issue, is now expected to spend at least the next week on the sidelines.
Atletico, currently down in fourth position in Spain's top flight, therefore have problems in central defence ahead of this weekend's La Liga clash against Celta Vigo, with Diego Godin also absent with a thigh problem.
"Jose Maria Gimenez could not train with his teammates in the last two sessions due to 'an infection in the subcutaneous cellular tissue of the right leg, which does not affect joints nor other structures'," read a statement from Atletico.
"The Uruguayan defender is undergoing a shock treatment with antibiotic to attack the infection."
Stefan Savic is Atletico's only fit senior centre-back ahead of the Celta clash.