A dominant performance was not rewarded until 12 minutes from time, when Pierre-Emerick Aubameyang slotted home the opener following a defensive error.
Henrikh Mkhitaryan added a second just a minute later, before young goalkeeper Timon Wellenreuther was caught in possession by Marco Reus, allowing the Germany international to roll the ball into an empty net.
The result extends Dortmund's winning streak in the Bundesliga to four games and leaves them eight points outside of the Champions League places.
"It was an absolutely perfect afternoon and a really great game for my team," Klopp told Dortmund's official website.
"From the first to the last minute we looked good with the ball, moving into the right places and showed outstanding counter-attacking pressing.
"In the first half we had plenty of chances, but unfortunately we couldn't convert them.
"It was important for us not to show any nerves and we finally made a breakthrough after 77 minutes."
He added: "I think that everyone wanted to jump on him when he scored. He had a really great game.
"It was the best game I've seen him play for Borussia Dortmund."
"When I look at the table, we are still only five points clear [of the relegation zone], even though we have won four games in a row," he continued.
"This shows what kind of situation we were in and where we still are. We must not let up now."
