The veteran midfielder underwent tests on Tuesday after training where he was revealed to have an irregular heartbeat.
A brief statement posted by Juventus claimed he hadn't travelled with the squad and had been diagnosed with atrial arrhythmia.
A statement read: "Sami Khedira has stayed in Turin for medical tests, from which emerged the opportunity to perform an electrophysiological study and eventual treatment of an atrial arrhythmia which appeared today [Tuesday]."
Juve boss Max Allegri had previously stated that the 31-year-old would be absent although was coy on providing a reason.
AF can lead to blood clots, stroke, heart failure and other complications if left untreated.
It is most common in people over the age of 65 but is often not life threatening.
Juventus travelled to Madrid earlier today ahead of their first-leg tie at the Wanda Metropolitano Stadium tomorrow.
Paulo Dybala is in line for a start despite a relatively disappointing campaign.
Allegri added: "I'll tell you now that Dybala plays,
"Paulo is in good shape. On Wednesday he needs his technique and his craft. On Friday, against Frosinone, he scored but played not as well as he has on other occasions.
"Even in terms of the team's level it was like this [not playing to their full potential], we created less. We will need a good display [against Atletico], with the awareness that we are facing a compact team that makes the most of set-pieces."
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