The defender's visible disappointment summed up a night in which Dortmund struggled to match their opponents' sharpness and conviction.
Their exit was sealed by a single first-half goal, scored by Ibrahim Maza after intelligent movement and neat interplay inside the box.
The young forward reacted quickest to a clever passage of build-up play, steering his effort past the goalkeeper to give Leverkusen a lead they would not relinquish.
Dortmund pushed for a response but found openings hard to come by, with Leverkusen's organised defensive structure limiting their attacking threat. As time ebbed away, the hosts maintained their composure, ensuring the margin remained intact.
Leverkusen's narrow victory propels them into the quarter-finals of the German Cup, continuing a promising run in the competition.
"We had a decent game, we needed to equalise before half-time, then it would have gone in a different direction. In the second half, we lacked a bit of punch," said Schlotterbeck, via ARD.
"Leverkusen simply scored one more goal and defended well. The two missed chances before half-time hurt. Then the game would have been more open.
"The game simply changed after Leverkusen's goal. They scored the opening goal, and the rest was bitter today. Nevertheless, we still want to achieve a great deal.
"We've done well in the league and we're sixth in the Champions League. But of course today hurts a lot. I'm also very downhearted. We now need a few days to recover, and then we'll carry on."