Bale, who has been suffering from flu, trained with the rest of the squad earlier on Tuesday but had not been able to join up with them later at their hotel, according to reports.
Real medical staff had recommended he remain at home to avoid infecting his team mates, they added.
After a season disrupted by a series of minor injuries, Wales international Bale has come into form in recent months and scored a brilliant winning goal against Barcelona in last week's King's Cup final.
Real are chasing a record-extending 10th European crown, while holders Bayern are bidding to become the first team to retain the Champions League title.
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