Leon Gortzka looked set to secure a well-earned point at Allianz Arena before Dortmund drilled Bayern after Dortmund had two minutes remaining.
However, Reus felt that the referee should have blown to dishonesty in the build-up and questioned whether officials would have come to the same conclusion that it was the other way around.
What happened in Der Klassiker?
Dortmund made an accurate start with Erling Haland twice within the first nine minutes.
Robert Lewandowski tapped home Leroy Sane's cross to bring Bayern back in the game, leveling the chance just before half-time.
Gortzka then put Bayern ahead to send the Bavarian giants back to the top of the table after completing their hat-trick moments ahead of Lewandowski for the first time in the match.
What did Reus say?
Dortmund felt that a foul was committed by Leroy Sane to Emer Cain before Bayern's third goal.
“To me, this is a blatant dishonesty,” he explained Sky Germany.
“I'll be honest: If it had been against Bayern, the referee would have whistled 100 percent. It's like that. Nothing to add.”
Thomas Muller narrated the incident when told about Reuss's comments. “I don't think we want such barriers to be blown for fouls in half the line,” he said. “Otherwise it would have stopped.
“I would not have seen it as a dishonesty against us, you can believe me or not. Nothing is worse when everything is always blown in the same way.”