The Uruguay international was forced off the pitch during his team's goalless draw at Alaves on Saturday.
"Jose Maria Gimenez has a grade I-II muscle injury in his right thigh adductor as was revealed by the MRI the Uruguay defender underwent on Monday," Atletico said in a statement on Monday.
No time frame has been given for his recovery but reports in Spain said the 22-year-old will be out of action for at least a month.
Gimenez will miss the King's Cup semi-final against Barcelona and could also be absent from the Champions League last 16 first leg at Bayer Leverkusen on Feb. 21.
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Atletico are fourth in La Liga, 10 points adrift of leaders Real Madrid.
(Reporting by Adriana Garcia, editing by Ed Osmond)
