Serge Gnabry sat out after testing positive for the coronavirus as Bayern looked for a positive outcome, whereas Atleti welcomed back Luis Suarez and Marcos Llorente amongst others.
The holders advanced into promising areas just after kickoff with Corentin Tolisso having Atletico goalkeeper Jan Oblak on his toes from a ball by Kingsley Coman.
Atletico had a chance to draw first blood three minutes to the half-hour mark when Suarez steered a square ball from Yannick Carrasco wide of the left-hand post after finding space outside the area.
The Bavarians seized initiative a minute later after Coman found space behind Kieran Trippier following a cross from Joshua Kimmich to beat Oblak from point-blank range.
Bayern carried a two-goal lead into halftime when Coman reversed roles on 41 minutes to play in Leon Goretzka who rifled the inside left of Oblak's goal following a deft first touch.
Joao Felix thought he had given Atleti a way back a minute from the break with a half-volley from a decent supply, but it was ruled out for offside by the Video Assistant Referee (VAR).
Tolisso put the LaLiga side out of reach on 66 minutes with a thunderous finish from outside the area after landing onto a loose ball from a free-kick.
Atleti's woes were compounded six minutes later when Coman completed his brace after running towards a pass from Thomas Muller for a composed finish.
Hansi Flick called for fresh legs a little later with an unassailable lead, as Douglas Costa and Bouna Sarr entered for Coman and Benjamin Pavard respectively.
Bayern ran down the closing minutes while Atleti pushed for some sort of consolation, as the defending champions cruised to victory.