The Spanish wing-back was withdrawn from the action in the first-half of the 1-0 victory, before being assessed by the club’s medical team on Friday.
Wolves doctor Matt Perry said: “In the first-half of the match with Olympiacos Jonny suffered an injury to his right knee.
“Yesterday a scan confirmed the first clinical impression of an injury to the anterior cruciate ligament which will require surgical repair.
“This has been arranged and the whole team wish Jonny well on his path to recovery.”
Young defender Lewis Richards is set to join up with the first-team squad as they travel to Germany tomorrow afternoon, ahead of Tuesday’s quarter-final against Sevilla.