After Dortmund's anger about a penalty not given at the Bundesliga summit in Munich, referee Daniel Siebert admitted a mistake.
"Penalty kick would have been the right decision," said the referee to "Kicker" on Sunday.
When the score was 1-2, Siebert decided to continue playing after a leg scissors from Bayern defender Benjamin Pavard against Jude Bellingham in the penalty area.
“In the running duel between Pavard and Bellingham, Pavard starts to straddle the ball to straddle the ball off his foot with his right leg.
This first attempt fails, Pavard does not play the ball, his leg instead represents an obstacle in Bellingham's path. Technically, it is a random bring and therefore a foul.
The fact that Pavard touched the ball shortly afterwards is irrelevant," Siebert said after viewing the pictures.
Borussia Dortmund coach Marco Rose was upset about the situation after the game.
"Of course I can do a somersault now, but I won't get a penalty for that," said the coach.
Dortmund lost 1:3.
Even in the first leg at 2: 3 at home, BVB was outraged by the referee's performance.
At that time, Felix Zwayer gave Bayern a penalty, but not Dortmund.
Then the excitement was so great that the referee withdrew for weeks.
Siebert also admitted to having been wrong in another controversial situation.
In the case of a hard challenge from Pavard against Julian Brandt, he "absolutely" should have shown a yellow card, said the referee.
"That was the biggest mistake in this game and I'm very annoyed about my assessment of this scene," said the 37-year-old.
Pavard only hit Brandt's ankle.
But he had "unfortunately had a wrong perception in the game".
"I'm glad that Brandt was able to continue playing and apparently wasn't seriously injured," said Siebert.
Bayern had secured their tenth German championship in a row by winning the top game.
After the lead by Serge Gnabry (15th minute) and world footballer Robert Lewandowski (34th), BVB shortened the lead with a penalty kick from Emre Can (52nd).
Jamal Musiala (83rd) made the final score.
In the middle of the hustle and bustle in Munich, BVB coach Rose announced a new title attack on permanent champion FC Bayern.
"We're talking about football.
And in football you can be champion ten years in a row, maybe 15,” he said.
"But there are always teams trying to change that - and we're one of them.
We will shake ourselves, rebuild again.”
This is also urgently needed for the designated second after a season with plenty of frustration in the Champions League, Europa League and DFB Cup.
Only the minimum goal of premier class qualification was achieved in the first year with the former Gladbacher Rose on the bench.
"First of all, you can congratulate Bayern for today," said Rose after the 1:3 and plenty of beer showers from the opposing series champions: "But I think we should all try to make the championship exciting and even more exciting next year and that tripping the German record champions.
Borussia Dortmund will certainly be one of the first to try that.”
BVB is working on being more competitive.
Defender Niklas Süle comes on a free transfer from FC Bayern and is supposed to help stabilize the shaky defense.
The national players Karim Adeyemi (RB Salzburg) for the offensive and Nico Schlotterbeck (SC Freiburg) for the defense are other fixed Dortmund additions.
As a possible successor to striker Erling Haaland, whose nagging future question should soon be finally clarified, there has already been speculation about the storm talents Hugo Ekitike (19) from Stade Reims or Adam Hlozek (19) from Sparta Prague.
"Dortmund is trying to upgrade a bit," said former Bayern boss Karl-Heinz Rummenigge appreciatively on the TV station Bild.
And they would still get money from the Haaland transfer in the till.
The Norway international can leave Dortmund early after this season thanks to a €75m release clause.
Manchester City are said to be in pole position in the race for the repeatedly injured storm giant.
"A move from Erling Haaland to the Premier League would not come as a complete surprise to us," said sporting director Michael Zorc on Sky.