The 25-year-old, who kept a clean sheet in a 1-0 first-leg success, was a late absentee from Friday's win over RB Leipzig due to a thigh problem, and reports have claimed that he only has a slim chance of recovering in time for the second leg.
Kobel joins a well-occupied Dortmund treatment room also holding Youssoufa Moukoko, Donyell Malen, Mateu Morey, Julien Duranville, Abdoulaye Kamara and Karim Adeyemi, whose sensational solo finish settled the first leg.
With Kobel struggling, Alexander Meyer should act as the last line of defence, with Niklas Sule and Nico Schlotterbeck forming an imperious central-defensive pairing in front of him.
Right-back Julian Ryerson must serve a one-game European suspension here, allowing a well-rested Raphael Guerreiro to return at left-back as Marius Wolf bombs down the opposite flank.
Emre Can came up with a phenomenal goal-line clearance in the first leg, and the ex-Liverpool man should form a recognisable midfield trident with Salih Ozcan and Jude Bellingham.
The absence of Adeyemi means that Dortmund stalwart Marco Reus is set to operate on the left-hand side, as Julian Brandt and Sebastien Haller complete the BVB attack.
Borussia Dortmund possible starting lineup: Meyer; Wolf, Sule, Schlotterbeck, Guerreiro ; Ozcan, Can, Bellingham; Brandt, Haller, Reus