Bayern Munich has confirmed the player will have an operation on a knee injury suffered in the DFL-Supercup defeat to Borussia Dortmund.
The Spain international fell to the turf after an innocuous-looking challenge with Marcel Schmelzer in the first half of Dortmund's 2-0 victory on Wednesday.
He indicated in the immediate aftermath he thought it was a serious injury and that was backed-up on Thursday when Bayern announced he would have to undergo surgery on a torn anterior cruciate ligament.
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A Bayern statement read: "Javi Martínez suffered a torn ACL in his left knee during the German Super Cup in Dortmund on Wednesday night and will not be available to coach Pep Guardiola for the remainder of the year."
It is a big blow for Guardiola who was expected to utilize Martinez's versatility to the full over the coming season.
The former Athletic Bilbao man can operate in midfield and defence and was an integral part of the Bayern side which won the Champions League in 2013 and retained the domestic double last season.
He was downbeat after hearing the news but vowed to return a better player, telling the club's official website: "Of course I am very sad but I need you not to worry - I'll come back even stronger."
Martinez is expected to fly to Colorado in the next few days to have surgery before returning to Germany to begin his rehabilitation.