The home team of the showdown, Bayern Munich took the lead in Der Klassiker at the Allianz Arena in the 15th minute.
German midfielder Joshua Kimmich whipped a corner to find Leon Goretzka, who headed the ball back to Serge Gnabry. German winger Gnabry was on the edge of the penalty box to control the ball with his thigh and unleash a right-footed shot that beat Dortmund goalkeeper Marwin Hitz.
Bayern Munich doubled the gap in minute 34 with Polish star Robert Lewandowski. Dortmund defender Dan-Axel Zagadou was under pressure to concede the possession of the ball. Thomas Muller passed the ball to unopposed Lewandowski as the Polish forward successfully netted the goal.
Bayern Munich led the first half 2-0.
Borussia Dortmund were awarded a penalty in the first minutes of the second half as Kimmich fouled Marco Reus.
Emre Can scored from the penalty spot to give hope to his team.
In the 83rd minute, Bayern Munich's 19-year-old midfielder Jamal Musiala made it 3-1 for his club, making a close-range finish.
Once the final whistle was blown, Julian Nagelsmann's men celebrated their success in the 2021-22 season.
Bayern Munich have 75 points in 31 matches to win their 32nd league title with three games to spare.
Second-place Borussia Dortmund have 63 points in the 2021-22 Bundesliga season that will end on May 14.