The Serbian international apparently suffered a torn calf muscle in a training session on Saturday.
Soon after, an MRI scan at La Manga hospital revealed the extent of the injury, and the club concluded that Subotić will be sidelined for up to six weeks.
Therefore, the defender will not be available for selection in the first couple of games at the start of the second half of the season.
With Subotić ruled out for the club's first Bundesliga game in 2013, Felipe Santana has emerged as the favourite candidate to replace him in the heart of the defence.
Borussia Dortmund will clash with Werder Bremen away from home in their first competitive game of 2013 on January 19.
In related news, merely days ago, Subotić and Sven Bender committed their futures to the club by signing new contract extensions with the club until 2016 and 2017 respectively, following the examples of Mario Götze, Mats Hummels, Jakub Blaszczykowski and Lukasz Piszczek, who have all recently signed contract extensions with Die Schwarzgelben.
Meanwhile, Ivan Perišić has left the reigning Bundesliga champions to join Wolfsburg, after the two clubs agreed to terms on Sunday. (ESPN)
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