The visitors took the lead at the Coface Arena through Pierre-Emerick Aubameyang and, although Maxim Choupo-Moting equalised from the spot, two Robert Lewandowski penalties secured Dortmund's victory.
Klopp had the likes of Mats Hummels, Neven Subotic and Marcel Schmelzer out with injury and was delighted with the character his side showed in front of another makeshift defence.
"We win with a full-back who has not played for six months [Lukasz Piszczek], and with a centre-back [Manuel Friedrich], who was [out for] almost eight months," he told Dortmund's official website.
"I am totally happy with the result and with the development of the game in view of a totally changeable situation.
"This was great fighting spirit."
The win ended Dortmund's two-game losing run in the Bundesliga.
They remain third, seven points behind leaders Bayern Munich, who also won on Saturday.