The incident occurred immediately after Pierre-Emerick Aubameyang scored what proved to be the winner for the visitors in the 64th minute and prompted referee Felix Zwayer to take both teams from the field, holding up play for around 10 minutes.
Schmidt claimed that a free-kick awarded to Dortmund in the build-up to the goal should have gone Leverkusen's way and was taken while the ball was still moving.
His protests incurred the wrath of Zwayer, who initially gestured that the 48-year-old should head to the stands and subsequently instructed Leverkusen skipper Stefan Kiessling to insist that his coach vacate the dugout.
While Schmidt did apologise after the game he also insisted he was entitled to stand his ground.
"I'm not one for gestures. I wanted to know why he wanted to send me off and I tried to discuss that with him, but it didn't happen,” he told reporters. "I wanted to have a reason.
"Maybe that was a bit stubborn of me, so I have hurt my team. I'm sorry. I am a role model and I've not done myself justice, but sometimes it is easy to react in hectic and emotional situations.
"My team fell behind to an irregular goal. I have the fourth official noting that the kick was executed a thousand per cent irregularly.
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"He [the referee] also did not give a thousand percent penalty and I'm just challenging for justice for my team."
Referee Zwayer, meanwhile, claimed that Schmidt's actions left him with no other option than to halt play.
"I tried several times to influence Roger Schmidt to leave the pitch area," he said.
"Since that did not happen, I had no choice but to interrupt the game."