The Spanish side were on course to record just their second win in the competition this season at Wanda Metropolitano Stadium, but were made to curse their luck when Muller converted from the penalty spot deep in the second period, after a foul by Felipe.
The result leaves Diego Simeone‘s side in second place with six points and his team needs of a positive impact in Salzburg, Austria to stand a chance in the last 16.
With qualification already in the bag for Flick’s side, the Bayern Munich coach made nine changes to his side to give some of his players a well-deserved rest.
Atletico began the brighter of the two teams testing Bayern’s post on occasions early in the game, but not able to find a way past Alexander Nuebel in the post.
The goal-keeper making his first Champions League start for Bayern was alert to save a 6th minute shot from Angel Correa after Felix released the winger. The home side continued to probe but were unable to cause any trouble the Bayern goal.
But their breakthrough came in the 26th minute with a goal from Joao Felix putting them ahead. The Portuguese attacker who has been bright in recent times, held his composure to score after he was found at the near post by a cross by Marcos Llorente.
With their first goal in the bag, the home team were content to patiently keep the ball and look for an opening in Bayern’s untested back-four. But none was to be found with Felix who hit the bar in the 58th minute from an offside situation the closet the home team went from doubling their lead.
Unable to double their lead and seal their win, Bayern were able to nick a point at the death with an 86th-minute penalty from Thomas Muller.
The result leaves Atletico with work to do in this group. They are back in action against Real Valladolid on Saturday while Bayern face RB Leipzig in a crucial Bundesliga match on the same day.