Jamal Musiala scored a hat-trick in a 17-minute span of the second half on Sunday in front of a crowd that unfurled a banner pronouncing "Smash FIFA!" while accusing the governing body of mismanagement.
Thomas Muller, Kingsley Coman and Michael Olise scored two goals each for the Bundesliga champions, who went ahead on Coman's goal six minutes in. Bayern had 17 shots on target to Auckland's one.
Musiala, a 22-year-old midfielder, replaced Harry Kane in the 61st minute, making his first appearance since April 4 after recovering from a hamstring injury.
He scored in the 67th minute, converted a penalty kick in the 73rd and scored again in the 84th.
Before a crowd of 21,152 at TQL Stadium, fans displayed a red-and-white banner referring to the 2015 raid by US law enforcement officers at a Zurich hotel that led to the arrest of many soccer officials: "10 Years Baur Au Lac — World Football Is More Poorly Governed than Before! Smash FIFA!"
Bayern built a 4-0 lead by midway through the first half when Sacha Boey scored in the 18th, Olise in the 20th and Coman in the 21st.
Muller, the 35-year-old who plans to leave Bayern this summer, added a goal in the 45th minute and Olise made it 6-0 in the third minute of first-half stoppage time.
Bayern will surely be tested more against Boca Juniors on Friday and Benfica on June 24 following this embarrassing mismatch.
"It is an unbelievable challenge to play against one of the world's best teams, and I think as the goals went in, obviously you get down on yourself and that gets more challenging. We did try our very hardest to keep them out," said Auckland forward Angus Kilkolly.
7°C