Exequiel Palacios volleyed the ball in with almost the last kick of the game from an Alex Grimaldo cross.
Despite topping their Champions League group, Borussia Dortmund have won just one of seven league games since October.
Borussia Dortmund are one win away from their first Bundesliga title in a decade, after two second-half goals from Sebastien Haller delivered a 3-0 win at Augsburg on Sunday
Bundesliga: Borussia Dortmund triumphed 1-0 in the derby against Schalke while Augsburg shocked Bayern Munich 1-0.
Bundesliga: Leaders Bayern Munich crashed to a shock 2-1 defeat at strugglers Augsburg on Friday without Germany midfielder Joshua Kimmich, who is back in quarantine after contact with someone who tested positive for Covid-19.
Bundesliga: A senior German politician has called to make it mandatory for all professional footballers in Germany to be vaccinated as the country struggles to contain a ferocious fourth wave of Covid-19.
Taiwo Awoniyi was stretchered off with his neck in a brace after a long delay while he received medical attention on the pitch.
Thomas Muller scored as Bayern Munich opened up a four-point lead at the top of the Bundesliga with a 2-0 victory over Augsburg at the Allianz Arena on Sunday.
Bundesliga: Erling Braut Haaland came off the bench to claim a hat-trick inside 20 minutes on his Borussia Dortmund debut and inspire a 5-3 comeback win at Augsburg.
A 4-0 win against Augsburg helps Bayern Munich take a big lead at the top of the Bundesliga table.
The Gabon star
Augsburg ensured their first win of the season when they overpowered Werder Bremen 3-1 to open the seventh round of Bundesliga at SGL Arena here.