I expected that, in the best-case scenario for Atalanta, they could steal a win by one goal or win the penalty shootout. Instead, they've proven to the world that they are no pushovers and are force to be reckoned with.
I suspect the fact that Atalanta is still fighting in the Serie A (with 2 more games to go), while Bundesliga has already concluded, has a pretty big effect on the result. It could be that Bayer subconsciously went into the relaxed, post-season mode, while Atalanta didn't lose their rhythm.
It could also be that the German team convinced themselves a little too much that they were invincible, which was reinforced by all the experts, fans and odds makers, and lost that underdog energy they started the season with. There's nothing worse you can do in any competition than to start celebrating before the game begins.