Dortmund made only one change from their thumping win over Augsburg, as Emre Can was recalled at the expense of Morey Bauza, who dropped out of the squad.
Can came close to giving BVB a perfect start in the fifth minute with a cracking strike from range that rattled the crossbar.
Erling Haaland had a good chance to give the visitors the lead in the 13th minute after latching onto a through ball over the defence but his shot was saved by shot-stopper Florian Muller.
Manuel Akanji almost broke the deadlock for Dortmund ten minutes before the break with a powerful strike from the edge of the box that missed the bottom corner by a whisker and Freiburg frustrated Edin Terzic's charges in the closing phase of the first stanza that ended goalless.
The hosts had a dream start in the second stanza as Woo-Yeong Jeong broke the deadlock for them four minutes from the break with a great strike from the edge of the box against the run of play, 1-0.
Jonathan Schmid doubled the lead for Freiburg three minutes later after goalkeeper Marwin Hitz failed to hold onto his strike from range and a difficult angle.
Youssoufa Moukoko almost pulled a goal back for Dortmund in the 63rd minute but his shot from outside the box hit the post, however, the German teenager eventually reduced the deficit for the visitors in the last quarter of an hour with a strike inside the box after a through ball by Haaland.
Moukoko came close to snatching the equaliser for Terzic's men in stoppage time after finding space inside the six-yard box but Muller pulled off a crucial save to earn Freiburg the three points that moved them up to eighth while Dortmund were left in sixth place.