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 German Bundesliga champions. 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.
"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," said Auckland forward Angus Kilkolly.
"We did try our very hardest to keep them out."
In Los Angeles, Paris Saint-Germain picked up right where they left off in their first match since winning the UEFA Champions League last month, turning what was billed as a blockbuster into a 4-0 rout of Atletico Madrid.
The sunsoaked midday match, timed to accommodate fans watching in Europe, drew 80,619 people to the sunsoaked Rose Bowl in Pasadena on a day when conditions led to water breaks in both halves.
"It's the best scheduled time for the European countries, but it's difficult to play in these conditions," PSG coach Luis Enrique said after the Group B clash.
Despite being without injured Ballon d'Or favourite Ousmane Dembele, the young team earned the win behind goals from four different players - Fabian Ruiz, Vitinha, Senny Mayulu and Lee Kang-in.
Elsewhere, Palmeiras drew 0-0 with FC Porto in New Jersey and Seattle fell 2-1 on home turf to Botafogo.
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