Jordy Hiwula struck first for his fourth goal in two games, but Bayern replied with a goal in each half to secure victory on their home turf.
Patrick Vieira’s men flew to Munich on Saturday for the second leg of their pre-season preparations, and will take on Nurnberg and Slovan Liberec in the coming days.
With Marcos Lopes, Sinan Bytyqi and Jorge Intima still away on international duty, and several of last season’s regular EDS stars away with the first team in the USA, there was just one change to the starting XI which triumphed so convincingly over HNK Gorica in Croatia 10 days ago.
Jack Byrne replaced Olivier Ntcham to take his place in a midfield triumvirate also containing captain George Glendon and Seko Fofana, while it was an all-English front three - Brandon Barker, Devante Cole and Hiwula were charged with doing the damage in the attacking third.
While training in the scorching Croatian sun went some way to preparing the City youngsters for 90 minutes of match action in the heat of the German afternoon, temperatures hitting the high 20s provided an extra challenge for those more used to the less than balmy nights at Hyde.
However, there was a fast tempo from the start as City immediately seized possession of the ball and rarely relinquished it in the first 15 minutes as their hosts sat deep and contented themselves with trying to hit the young Blues on the break.
Angelino and Barker reprised their connection on the left hand side which led to such rewards for the u18s last season, and repeatedly troubled the Germans on the flank.
Meanwhile, Angus Gunn was forced to pull off a good stop to deny Steeven Ribery, who showed off some of the genetic talent that have made older brother Franck such a vital player for the German side’s first team.
While Bayern looked to be in the ascendency as the half hour mark approached, it was City who dealt the first blow, as Cole showcased his predatory instincts to seize on a loose ball and unselfishly feed Hiwula, who had the simplest of tasks to tuck the ball into an empty net.
However, the hosts poured forward in search of an immediate reply, and the lead lasted less than five minutes, when centre back Edwin Schwarz nodded in the equaliser from a corner.
City remerged revitalised after the half time break and the start of the second period mirrored the first as City held onto the ball and created plenty of chances through Angelino and Barker, who continually caused problems for Bayern with their pace out wide.
Cole might have given City the lead again on 58 minutes, and both he and Bossaerts had good chances from a set piece but were thwarted by the athletic reflexes of David Hundertmark in the opposition goal.
But in a tight and intriguing encounter, momentum against swung back towards Bayern Munich, and Gunn had a intervene on a number of occasions before Tobias Schweinsteiger had a goal chalked off for offside with 20 minutes left.
It began to look like the game would end all square as the tempo from both sides dropped a notch as the heat of the day and intensity of the first 60 minutes took their toll on legs still mid-way through pre-season preparations, but instead there was a late sucker punch.
With just five minutes left Lukas Gortler crossed from the left and Schweinsteiger headed past Gunn to seal the win for the hosts.
Vieira will have been encouraged by the problems his young side posed for a strong Bayern Munich side, but will be seeking an immediate return to winning ways when City take on Nurnberg on Wednesday.
CITY: Gunn, Smith-Brown (Bossaerts 60), Angelino, Bryan, Maffeo, Glendon (c), Byrne, Fofana, Cole, Barker (Pozo 66), Hiwula.
