This is the first time Dortmund have lost to Freiburg in Germany's top flight for 11 years with Saturday's setback coming just four days after losing 3-1 to Bayern Munich in the German Super Cup.
Freiburg raced into the lead when dead-ball expert Vincenzo Grifo blasted in a superb free-kick after just six minutes.
Dortmund thrashed Eintracht Frankfurt 5-2 last Saturday on the opening weekend, but the visitors' defensive frailties emerged again having been a problem last season.
After England midfielder Jude Bellingham lost the ball, Freiburg forward Roland Sallai was left unmarked to smash home his shot as the hosts doubled their lead on 53 minutes.
Bellingham made amends by pressuring the defence with a strong run which caused Freiburg midfielder Yannik Keitel to put the ball into his own net with half an hour to go.
Freiburg had been winless in their previous 19 meetings with Dortmund dating back to May 2010.
Standout matches today