The hosts took the lead against Schalke through Mario Gotze, but saw both Marco Reus and Marius Wolf sent off while Daniel Caligiuri hit twice to send his team on the way to victory.
But it was Caligiuri's first strike from the spot which drew the wrath of BVB coach Lucien Favre, who could not believe his team was sanctioned for a seemingly innocuous handball.
"That's a joke. Nobody has a plan of football. It's the biggest scandal that nobody knows anything about it," he fired after the game.
"What do they want to happen? Should the players cut off their arms and run without them?
"The red cards? We have to avoid these situations. But we need to admit that the referee didn't have his best day"
Marco Reus & Marius Wolf were given their first red cards vs Schalke.— Goal (@goal) 27 de abril de 2019
They were Dortmund’s 99th and 100th red cards.
Someone really doesn’t want them to win Bundesliga this season 🙃 pic.twitter.com/pUAC5Fnwsq
Schalke trainer Huub Stevens agreed that the kick should never have been given in a rare show of solidarity with his opposite number.
"I think it's very disgusting that a penalty like this has been given," Stevens signalled.
"I told Lucien Favre that I am not happy with it as well. But my team received these kind of decisions against us in the weeks before."
The referee's decisions were not the only talking point to emerge from the game.
Dortmund youngster Jadon Sancho received treatment after being struck with a cigarette lighter thrown from the stands while no less than five Schalke players finished a bad-tempered derby with yellow cards.
And speaking after the final whistle, Favre admitted that his team's title aspirations may have been extinguished.
"Yes, of course," he replied when asked whether the bid to topple Bayern Munich had come to an end.
Bayern continue to lead Dortmund by one point at the Bundesliga summit having played one fewer game.
Victory over Nuremberg on Sunday would open up a four-point lead with just three rounds of the season remaining, putting the Bavarians on course for their seventh consecutive title.