Pierre-Emerick Aubameyang opened the scoring on 31 minutes against the Bundesliga's bottom side, who levelled early in the second half through Benjamin Kessel.
Aubameyang earned Dortmund, who are third in the league, victory with a neat left-footed finish on 65 minutes.
Klopp praised his team for their attitude against the struggling side, but would have liked to have the result sealed earlier.
"We are Borussia Dortmund and we are ready to work for three points. It doesn't matter where it is, against whom, or when. That's what we had to prove this evening," he said.
"Our opponent challenged us to the maximum. The opponent was well positioned. The opponent is dealing with its own situation incredibly well.
"And, as I've experienced previously, because the atmosphere was great. To make this job easier you need to use your chances.
"We didn't do that to the extent that we've managed to do in the past. That's why the game stayed tight and became even tighter after the equaliser."
Klopp was just pleased with the win, which lifted Dortmund to within a point of Bayer Leverkusen and 14 from Bayern Munich.
"We carried on working. We managed to create some great chances that, as I said, we didn't use," he said.
"We left men open, hit the post and what not but we won today against a strong opponent. It feels really good."
