The Spain international will undergo surgery after sustaining the injury during Bayern's 2-0 defeat to rivals Borussia Dortmund in the DFL Supercup on Wednesday.
Martinez was carried from the field on a stretcher after 30 minutes after attempting an acrobatic volley.
Bayern have subsequently confirmed the severity of the 25-year-old's injury and he will not play again in 2014.
"Javi Martinez has suffered a cruciate ligament tear and will be operated on soon in the USA. He faces several months out," read a post on Bayern's official Twitter account.
Bayern added a further statement on their official website, which read: "Javi Martinez suffered a torn ACL in his left knee during the Supercup against Dortmund on Wednesday and is therefore no longer available in this year."
Speaking on the setback, Martinez added: "Of course, I am very sad. But you need not worry, I'll come back even stronger."
Martinez moved to the Allianz Arena from Athletic Bilbao in August 2012 and made 18 Bundesliga appearances for the German champions last term.
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