Having clinched an eighth straight title 11 days earlier, Bayern finally got their hands on the trophy following a comfortable victory at the Volkswagen Arena on the final day of the season.
Muller laid on a record 21st assist of the season as Kingsley Coman got Bayern up and running, before Mickael Cuisance doubled their advantage on the stroke of half-time.
Josuha Guilavogui was shown a second yellow card for a foul on Cuisance and Robert Lewandowski scored the resultant penalty in the 72nd minute, with Muller adding Bayern's 100th Bundesliga goal of the season in the closing stages.