Neuer, Ribery and Dante came in at 62'
Boateng, Gotze, Lahm, Muller, Badstuber, and Schweinsteiger came in after the 80' mark.
You want to tell me those 9 players wouldn't make a massive difference in ANY lineup? You could probably play 3 of them for the whole game and get a much more favorable result for Bayern.
My favorite anecdote from the game was Pep afterwards politely asking for a rematch where they would prepare better and play their starters more. Obviously, the MLS did not do that. I don't know if MLS had contractual obligations with other clubs, but I am relatively confident that Pep was determined to lay an epic woodshedding on the MLS if the rematch happened.