Raul Bobadilla's goal early in the second half settled matters at the Westfalenstadion, where Dortmund hoped its season might finally take off, only to discover instead that its survival battle seems set to go the distance.
Fans vented their anger at the end of the match, with Mats Hummels and Roman Weidenfeller more than happy to approach them and listen to the feedback.
As @BVB Dortmund stay bottom, Weidenfeller and Hummels discuss the match with their furious fans. https://t.co/JQEEBFL3z2 — BT Sport Football (@btsportfootball) February 4, 2015
Augsburg, on the other hand, celebrated a win which keeps it level on points with third-placed Borussia Monchengladbach, and on course for a place in Europe.
The Bavarian side was unfortunate to lose in the reverse fixture at the start of the season with Dortmund surviving a late storm to hold on to a 3-2 win.
The visitor tried to make things difficult for Dortmund with Ji Dong-Won, back with Augsburg for a second time, lobbing Roman Weidenfeller and, unfortunately for him, also the crossbar.
Dortmund thought it had taken the lead in the 26th minute when Pierre-Emerick Aubameyang got a touch to Ciro Immobile's shot to ensure it crossed the line, but the assistant referee's flag soon went up.
Augsburg silenced the 80,000 fans inside the Westfalenstadion five minutes into the second half when Halil Altintop dribbled the ball through the Dortmund ranks before the ball fell to Bobadilla, who drilled it past Weidenfeller.
Dortmund's hopes of recovering received a boost when Janker was shown a straight red card for fouling Aubameyang as the last defender.
But all that was left for Augsburg to do was defend its advantage, which it succeeded in doing with just a few scares.
Henrik Mkhitaryan wasted one before Immobile headed straight at Alexander Manninger from close range, summing up Dortmund's season of near misses and disappointments.
Bayer Leverkusen continued its own bid for a top-four finish with a 1-0 win away to relegation-threatened Hertha BSC.
Elsewhere at the bottom, Hamburg emphatically ended a barren run of four games without a goal with a crushing 3-0 win at fellow struggler Paderborn.
A second-minute penalty from captain Rafael van der Vaart saw the visitor on its way, before second-half strikes from Marcell Jansen and Zoltan Stieber wrapped up the win, which gives Josef Zinnbauer's side a two-point cushion above the relegation zone.
Meanwhile, Paderborn has now recorded just one win in its past 11 Bundesliga outings.
Werder Bremen secured its third straight win with a 2-1 victory at Hoffenheim, while Cologne was held to a 0-0 draw at home to Stuttgart.
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