With the likes of Paul Pogba, Romelu Lukaku and Jesse Lingard still not available following their World Cup exertions, Mourinho again turned to academy graduates James Garner, Axel Tuanzebe, Tahith Chong and Demetri Mitchell for the second half.
Despite suffering defeat in Bavaria, the United boss felt proud that his mix-and-match side more than held their own for large parts.
"Finally, it's over. Finally, such a difficult pre-season is over," he told the club's official website. "The players were, once more, brilliant. They could not have done better than what they did. It was a fantastic experience for the boys.
"There was a moment I was looking to the area and there was Axel at centre-back to left, Demetri at left wing-back, Garner in midfield on the left and Chong. At the same time it was [Robert] Lewandowski on Axel, [Arjen] Robben on Mitchell, [Leon] Goretzka on Garner and [Niklas] Sule on Chong.
"It was fantastic, absolutely fantastic. We were playing against their best team, it was their complete squad apart from [Corentin] Tolisso."
United's Premier League season begins with a home match against Leicester City on Friday evening.