The 44-year-old has confirmed that the Serbian centre-half will be out of action after picking up a facial injury in the victory against Felix Magath's men
A brace from Mario Gotze and solitary strikes by Shinji Kagawa, Sven Bender and Robert Lewandowski gave the champions a convincing victory, although Subotic's misfortune following collision with Sotiris Kyrgiakos was a sour note for Jurgen Klopp.
The injury will be a big blow for the German club who are competing on three fronts in the Bundesliga, the Champions League and the DFB Pokal.
"Neven needs surgery and will be out for up to six weeks. This throws a shadow over the game," the coach told Kicker after the game.
Despite Klopp's disappointment with the injury to Subotic, the coach was delighted with the team's performance against Felix Magath's men.
"This was a really good game from my team who showed great movement and pinpoint passes throughout. A brief moment of arrogance has left us without a clean sheet yet the team has shown a great response," he added.
The win for Dortmund lifts them into second place, two points behind Bayern Munich who face Augsburg on Sunday afternoon.