Subotic was substituted a minute before the break in Dortmund's 2-1 defeat to Wolfsburg after landing awkwardly following a collision with Ivica Olic.
The Serbia international will undergo an MRI scan to determine the extent of the injury, with coach Jurgen Klopp explaining he has "probably torn the cruciate ligament", adding that the injury is "terrible news".
On the match itself, Klopp was left frustrated, citing minor incidents that went against his side - along with a superb strike from Olic - as the main reason behind the defeat.
"It was a tight game in the first half where we had some, but too few, good moments," he told the club's official website.
"We gave away too many free-kicks, which allowed the opposition some practice in taking them.
"Olic's goal was a dream. It should have been blocked, but that didn't happen.
"We have tried everything, but in tight situations, everything went against us."
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