Vladimir Darida converted a penalty five minutes into the second half after Mergim Mavraj handled Admir Mehmedi's cross to move Freiburg up to 16th with eight points, leaving Dortmund and Werder Bremen in the bottom two with seven each.
Dortmund, champions in 2011 and 2012 and runners-up in the last two seasons, have won only two Bundesliga games this season and have lost their last five, although they top their Champions League group with a 100 percent record.
Earlier, Borussia Moenchengladbach handed Hoffenheim their first Bundesliga defeat of the season and kept the pressure on leaders Bayern Munich with a 3-1 win, helped by a Patrick Herrmann brace.
Gladbach, unbeaten this season after 17 games in all competitions, stayed third with 20 points, behind VfL Wolfsburg on goal difference and four points adrift of Bayern, who beat Borussia Dortmund 2-1 on Saturday.
The Foals went ahead after 12 minutes when a slick counter-attack ended with Andre Hahn firing home from Herrmann's pass.
Gladbach eased off and Anthony Modeste equalised after half an hour, but it only took three minutes for the hosts to regain the lead with Hahn this time providing the cross for Herrmann, who was quickest to react and scored from close range.
Herrmann struck again in the 52nd minute, snapping up a rebound after Oliver Baumann parried Havard Nordtveit's low, powerful free kick from 25 metres.
Hoffenheim had little to offer after that and Gladbach cruised to their fifth league win in 10 matches this season.
Promoted Paderborn beat Hertha Berlin 3-1 in Sunday's other game, leaving the visitors as the only team without an away win.
(Writing by Brian Homewood in Berne; Editing by Rex Gowar)
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