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The Germany international aggravated an old knock shortly before half-time during Jupp Heynckes' side's LIGA Total! Cup match against Werder Bremen on Saturday, and it emerged after the game that he would need surgery to repair his ankle.
The 27-year-old is now certain to miss the start of the Bundesliga season, with the recovery time for such an operation between four and six weeks.
"He faces four to six weeks of rest, of which three of those he will be on crutches for. The damaged cartilage must be smoothed," sports doctor Bernd Kabelka told Bild.
Gomez will join David Alaba (stress foot fracture), Rafinha (torn knee ligament) and Diego Contento (fractured foot) on the sidelines for Bayern, although the club were handed a boost by the news that Bastian Schweinsteiger's ligament strain is not as serious as first feared.
"He will need to rehabilitate for two days but then he will be able to exercise again," Heynckes confirmed.
Die Roten start their Bundesliga campaign away to Greuther Furth on August 25, and face arch-rivals Borussia Dortmund in the DFL Supercup on August 12.