With Dortmund desperate for a new striker following Erling Haaland’s transfer and Sébastien Haller’s health issues, head coach Edin Terzic moved during the week to sign Anthony Modeste (34) from Cologne and had no hesitation in giving him his debut.
Freiburg, meanwhile, included former Dortmund defender Matthias Ginter in the starting XI.
It was a tepid start to the game, with both sides in a cagey mood. Freiburg had some joy down the left flank as Vincenzo Grifo linked up well with Christian Gunter, but not enough to truly trouble the Dortmund defence.
Despite the tentative initial exchanges, Grifo forced a good save from Dortmund goalkeeper Gregor Kobel - with Freiburg scoring 24 goals from set-pieces last season in the Bundesliga, the visitors needed to be fully concentrated in such situations.
Soon after, Michael Gregoritsch netted his second goal in as many games with a wonderfully-placed header to give Freiburg the lead ten minutes before half time.
With Dortmund now chasing the game, Terzic decided upon a change at the break, bringing on Marius Wolf for right back Thomas Meunier, who struggled during the first period.
Freiburg, though, kept the pressure on the Dortmund defence on the few occasions where they countered, especially former player Nico Schlotterbeck.
It was his mistake that very nearly led to the home side grabbing a second goal, however Kobel saved well from Roland Sallai’s shot.
Just as Christian Streich’s men looked to be closing in on the three points, Dortmund equalised out of nothing with 13 minutes to go.
A speculative 25-yard shot from substitute Jamie Bynoe-Gittens looked harmless, but Freiburg goalkeeper Mark Flekken spectacularly spilt it into the net.
Inside the final 10 minutes, Moukoko dispatched a low shot into the corner from close range to complete the comeback, and the visitors then confirmed all three points when Wolf fired home from inside the penalty area.
A great result for Dortmund, but Streich will be bitterly disappointed to lose when his team looked in full control. Check out the full game summary with Flashscore.
Flashscore Man of the Match: Marco Reus (Borussia Dortmund)
