The Schalke coach saw Bastian Schweinsteiger and Mario Mandzukic score in the 21st and 22nd minutes respectively, and from there the Bavarians never looked back, as further goals from Franck Ribery and Claudio Pizarro completed the win.
Keller was pleased with the way his side had started, but he conceded that it was effectively game over once Mandzukic had doubled the champions' lead at the Veltins Arena.
"We started very well, had a good 20 opening minutes but then we got hit twice and never recovered after that," he said.
"We had imagined this differently. To lose 4-0 at home is a flop."
Schalke captain Benedikt Howedes had no complaints about the result and also felt that the writing was on the wall after the first two goals.
Asked about the task of coming from two goals down, Howedes said: "It is of course extremely difficult.
"We tried everything again in the second half, but in the end, we must acknowledge that Bayern deserved to win. (The first) 20 minutes was not good enough."
