Bayern, who already clinched the Bundesliga title by 13 points, added their second piece of silverware this season with the victory over Leverkusen, which included a Robert Lewandowski double.
The Bavarian club are also still in contention for the UEFA Champions League which would cap a remarkable season.
However, Bayern boss Hansi Flick wanted his side to enjoy the moment, before casting their minds onto the continental competition.
“The way the team played in the last few weeks was sensational, the attitude is just fantastic,” Flick said.
“It’s nice to see the players believe in their own strength. We’re just very happy. What this team is achieving is extraordinary.
“In the second half there were a few things we want to improve. But today the only thing that counts is the joy at the double.
“The players can wind down for a few days now, and then we’ll prepare for the Champions League.”
Early goals from David Alaba and Serge Gnabry earned Bayern a 2-0 lead inside 25 minutes and they never looked back despite Leverkusen’s late rally.
Bayern stalwart Thomas Muller admitted the title felt strange with the final played without their fans in the stadium.
“It’s really a bit of a sad moment, the league is our bread and butter, of course we wanted to get that over the line, but when the fans are missing in such a thing as a cup final - I paused for thought at the end at the awards ceremony,” Muller said.
“It just doesn’t feel the same.”