The 28-year-old Reus had been in great form with three goals in five league games since mid-February after nine months sidelined by torn knee ligaments.
However, Reus is struggling after playing nine games in a little over a month and, having picked up a groin injury, trained alone this week.
“That’s why I don’t think he will make it this weekend,” admitted Dortmund head coach Peter Stoeger, who is unbeaten in his 12 league games since taking charge in December.
Reus, who missed the 2014 World Cup with torn ankle ligaments and Euro 2016 with a groin strain, is desperate to play at Russia 2018 in June.
He was left out of Germany’s friendlies against Spain and Brazil, who play at Berlin’s Olympic Stadium on Tuesday, to focus on his club form.
Third-placed Dortmund, who are 18 points behind leaders Bayern in the table, want a win at the Allianz Arena to spoil Bayern’s title party.
If second-placed Schalke fail to beat Freiburg in Gelsenkirchen and Bayern are victorious against Dortmund, the Bavarians will be crowned German league champions for the sixth straight season.
Stoeger said Japan midfielder Shinji Kagawa is expected to miss the next two weeks with an ankle injury.
Ukraine winger Andriy Yarmolenko, who has a foot injury, is only expected to return towards the end of the season.
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