The S04 boss has bemoaned his team's "extraordinarily bad" performance against Pep Guardiola's team on the back of their 6-1 thrashing at the hands of Real Madrid in Europe
The Gelschenkirchen outfit were 4-0 down inside half an hour at the Allianz Arena, with Arjen Robben netting twice, while David Alaba and Mario Mandzukic also got their names on the scoresheet.
An own goal from Rafinha brought a second-half consolation for Schalke, but Robben deservedly grabbed his hat-trick and Bayern's fifth from the penalty spot in the 77th minute.
The embarrassing loss came just three days after Schalke were thrashed 6-1 at home to Real Madrid in the first-leg of their last-16 Champions League tie and Keller was unable to hide his frustration.
"It was an appalling first half. It was catastrophic. It really was an extraordinarily bad performance," he told Sky. "We fell apart. We conceded a deflected goal after two and a half minutes. You could see from then on we hadn't put Wednesday's defeat to Real behind us.
"We were frightened and did none of the things we'd said we would do. We owe our fans an apology. We had more courage in the second half. It's okay to lose here, but not like that."
Despite the crushing defeat, Schalke had previously gone seven league matches without a loss, with Keller's men clinging on to fourth spot, two points ahead of fifth-placed Wolfsburg.