The Spain international was withdrawn in the second half of the 1-0 quarter-final second-leg loss to the Portuguese side in Lisbon and was sent for further tests.
"After undergoing medical exams this Friday, April 13, he has been diagnosed with a hamstring injury to his left leg," Atleti confirmed in a statement via their official website.
The club were unwilling to put an estimated time frame on the former Chelsea forward's recovery.
Atlético have already played an English club in the #UEL semi-finals, eliminating Liverpool on away goals in 2009/10 on their way to lifting the trophy (1-0 home, 1-2 away)...#UELdraw pic.twitter.com/0NERmCfiaQ— UEFA Europa League (@EuropaLeague) April 13, 2018
Atleti will hope to have the 29-year-old available for the first leg of their Europa League semi-final tie against Arsenal at the Emirates Stadium on April 26.