Dortmund had not gone beyond the group stages since 1998 before this year, while this is Malaga's debut Champions League season.
As such, Klopp said that there will be at least one "surprise team" in the semi-finals this season.
"Borussia Dortmund and Malaga are two teams that have surprised with their performances in the Champions League this season," UEFA.com quotes Klopp as saying.
"So one thing is certain, there will be a surprise team in the semi-finals. The way they eliminated Porto shows they have a lot of quality in their squad."
Dortmund beat Shakhtar Donetsk to reach this stage.