Morata twisted his knee during Wednesday’s session with Diego Simeone’s squad and tests confirmed a “moderate sprain”.
A timescale has not been placed upon the 26-year-old’s recovery at this stage but he will sit out training on Thursday.
Atleti have started their LaLiga campaign with back-to-back 1-0 wins over Getafe and Leganes.
Spain international Morata scored in the first of those matches but missed a second-half penalty.
Simeone’s men are back in action at home to Eibar on Sunday.