Marco Reus' fourth-minute penalty was ultimately enough to see off Mirko Slomka's side at Signal Iduna Park, but otherwise they failed to beat Ron-Robert Zieler in a nervy encounter.
Klopp was without long-term injury victims Ilkay Gundogan (back) Sebastian Kehl (foot) and Lukasz Piszczek (hip), with key defender Mats Hummels suspended for the clash.
And the coach also hinted that the recent international break had resulted in the disjointed performance, with his squad unable to train with each other as a whole for almost a fortnight.
"The game reflects the problems of the last 13 days," he told the club's official website.
"We played well up until we ran out of steam. Then we stopped playing football, with one reason being the physical shape of the players.
"Nuri (Sahin) or Marco (Reus) have a training deficit, and for them it was really hard work. But we also let them impose their game on us and played a lot of long balls forward.
"It was a really hard-fought win, but that's okay.
"One can also see this game as an extra training session, one we missed due to the (international) break.
"We have to get through it, but it will only make us stronger.
"The fans supported us fantastically. We now have to shake ourselves up and take a deep breath."