Javi Martinez scored the only goal at the Allianz Arena, glancing home a second-half header from a corner, while Bayern forward Arjen Robben had a late strike ruled out for offside.
United, who start their league campaign at home to Leicester on Friday evening, were captained by Alexis Sanchez in Bavaria.
The Chile forward was supported in attack by Juan Mata, Marcus Rashford and Andreas Pereira, with recent signing Fred partnering Ander Herrera in central midfield.
Jose Mourinho brought a host of youngsters off the bench in the second half, including Tahith Chong and Axel Tuanzebe, while goalkeeper Lee Grant, signed from Stoke in July, came on for David de Gea.
United created little during the match and were unable to find an equaliser in the closing stages.
Sergio Aguero has become the first player to score 200 goals for Manchester City, extending his own club record to 201 after bagging a brace in the Community Shield against Chelsea.
Here, Press Association Sport looks at some of his memorable and milestone goals.
Numbers one & two
v Swansea, Premier League – August 15, 2011
An impressive debut, netting twice to launch an ultimately successful title charge with a 4-0 win. First was a tap-in at the back post, with a long-range
v Wigan, Premier League – September 10, 2011
Showed great composure when through on goal to complete his first hat-trick for City.
v West Brom, Premier League – April 11, 2012
Opened the scoring in a 4-0 victory with a long-range shot from outside the box after a driving run, his first of two on the day.
v QPR, Premier League – May 13, 2012
His most famous strike, pouncing deep into injury time as City snatched Premier League title glory in the most dramatic fashion.
v Manchester United, Premier League – April 8, 2013
Came off the bench to net a late winner at Old Trafford with a superb solo effort.
v Manchester United, Premier League – September 22, 2013
Brought up his half-century in just his 74th appearance with the first of a double in a 4-1 win over City’s arch-rivals, hooking in a volley from six yards out.
v Bayern Munich, Champions League – November 25, 2014
Completed a memorable hat-trick and a famous victory over Pep Guardiola’s Bayern after pouncing on a mistake in the 89th minute.
v Manchester United, Premier League – April 12, 2015
Notched another landmark goal in a clash with the neighbours by firing a close-range shot through the grasp of David de Gea for the second of another derby double – but it provided consolation only in a 4-2 loss.
v Newcastle, Premier League – October 3, 2015
Delivered a masterclass in finishing to destroy Newcastle with five goals in the space of 20 minutes, equalling a competition record for the most goals scored by an individual in a match. Were it not for an injury-enforced substitution, he might have had the chance to net a record sixth.
v Newcastle, Premier League – April 19, 2016
The goal should have been disallowed for offside – but the headed opener in a 1-1 draw at St James’ Park was Aguero’s 100th in the Premier League. Coming in just his 147th Premier League appearance, he was the second-fastest player to reach that milestone behind Alan Shearer – Harry Kane has since split the duo.
v Middlesbrough, Premier League – November 5, 2016
Sidefooted home an inviting cross from Kevin De Bruyne.
v Napoli, Champions League – November 1, 2017
The goal that saw him become City’s record goalscorer, overtaking Eric Brook’s long-standing tally of 177. Aguero picked up an attack after Leroy Sane was dispossessed, driving forward and shooting home from the edge of the box. Helped City to a memorable victory at the San Paolo stadium.
v Bournemouth, Premier League – December 23, 2017
Headed home a Fernandinho cross to become the first City player to reach 100 goals in games at the Etihad Stadium. It was his first of two on the day.
v Chelsea, Community Shield – August 5, 2018
Aguero’s latest landmark goal came at Wembley, after good work down the left by Phil Foden. Aguero added goal 201 later in the game
Wayne Rooney saw a free-kick strike the woodwork as DC United drew 1-1 with the Montreal Impact – but remain bottom of Major League Soccer’s Eastern Conference.
The Canadian side took an early lead, with Matteo Mancosu getting a fortunate bounce before burying the ball into the net after five minutes.
Rooney curled a free-kick which beat goalkeeper Evan Bush but hit the post and United finally got an equaliser after 70 minutes through Yamil Asad.
The Seattle Sounders left it late in their 2-1 win over Minnesota United.
Darwin Quintero slotted the ball into the net after 19 minutes at TCF Stadium, but the Sounders were awarded a penalty with 90 minutes gone after Miguel Ibarra handled the ball defending a Roman Torres header.
Nicolas Lodeiro fired the spot kick home and Will Bruin lobbed Bobby Shuttleworth in the seventh minute of stoppage time to seal an unlikely win.
Josef Martinez scored a brace as Toronto FC drew 2-2 with Atlanta United, Orlando City had an injury-time equaliser in a 3-3 draw with the New England Revolution, and San Jose Earthquakes had two from Vako in a 3-1 win over FC Dallas.
Erik Hurtado scored with three minutes left as the Vancouver Whitecaps drew 2-2 with New York City FC, Colorado Rapids also scored late to beat the LA Galaxy 2-1 and Diego Rubio’s 74th minute effort was enough to see Sporting Kansas City beat the Houston Dynamo 1-0.
Real Salt Lake won their first game in four 2-1 over the Chicago Fire with Bastian Schweinsteiger’s effort cancelling out Damir Kreilach’s opener, before Kreilach got his second, and the Portland Timbers beat the Philadelphia Union 3-0.