A late strike from Robert Lewandowski ensured that Jurgen Klopp's men delayed Bayern Munich's inevitable lifting of the Bundesliga title, after Alexandru Maxim cancelled out Lukasz Piszczek's opener.
However, the game was marred by a number of aggressive tackles, with Marcel Schmelzer substituted with a suspected broken nose - leaving BVB defender Subotic to criticize the home side.
"Men's sport must always be fair. I don't try to ram an elbow into an opponent, because that's not manly, everyone can do that, a woman can do that," Subotic told the club's official website.
Bender was equally unimpressed with VFB, but praised his teammates for their fighting spirit.
"It was a very difficult game," the 23-year-old said. "VfB gave their all, they were committed and pushed the limits of what's allowed. But I think we fought back well - but within the rules of the game."
Former BVB star Michael Zorc defended the referee for his part in proceedings but believes a pattern is emerging in clashes between Dortmund and Stuttgart.
"In the first game it was [Sebastian] Kehl, now it was Schmelzer who suffered a broken nose," Zorc said. "I don´t think it was intended but a foot doesn't belong there. After the game everyone was lying on a massage table. The referee is not to blame, he had a tough job. We are happy about the three points."