However, the victory was not enough for Jurgen Klopp's side to retain their slim chances of winning the title, as Bayern Munich's 1-0 away triumph over Eintracht Frankfurt saw them regain the championship.
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Last season's German champions made the better start to the contest and surged ahead midway through the first half through Julian Schieber, who took advantage of a defensive slip-up to smash home.
Dortmund had a number of chances to increase their advantage and were stunned to concede twice in the final two minutes of the half.
Daniel Baier equalised for Ausgburg on 43 minutes when he volleyed home from 30 yards and moments later Kevin Vogt tapped home from close range after Mitchell Langerak kept out Tobias Werner's attempt.
However, Klopp's side came back strongly in the second half and restored parity seven minutes into the restart, Robert Lewandowski and Jonas Hofmann combining to set up Schieber, who scored from just yards out for his second goal of the afternoon.
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Moments later Jan Moravek squandered a great opportunity for Augsburg as he raced through on goal following Marcel Schmelzer's mistake, but his final effort was cleared off the line by Felipe Santana.
Lewandowski's headed goal from a Nuri Sahin free kick in the 70th minute was ruled out because of offside, but the Polish striker etched his name on the scoresheet in injury time.