After being frustrated over and over again by Schalke goalkeeper Timon Wellenreuther, Pierre-Emerick Aubameyang broke the deadlock in the 78th minute before, a minute later, Henrikh Mkhitaryan sealed victory.
Marco Reus added a third as Dortmund gave a more realistic look to the result of a one-sided Revierderby.
Meanwhile,??Bayer Leverkusen built on their midweek Champions League win over Atletico Madrid by beating struggling Freiburg 1-0 at the BayArena.
Simon Rolfes scored the only goal of the game as Roger Schmidt’s men got back to winning ways to move above both Augsburg and Schalke into fourth place.
Defeat saw Freiburg slip into the bottom two, where they join Baden-Wurttemberg rivals Stuttgart for at least the next seven days.
Hannover and Stuttgart both had a man sent off as their at the Niedersachsenstadion finished in a 1-1 draw.
Christian Gentner gave bottom-placed Stuttgart the lead, but Lars Stindl levelled for the hosts.
Stindl was then given his marching orders, with Martin Harnik also seeing red as tempers flared at the death in Lower Saxony.
It was a good day for Hoffenheim as they moved to within two points of the top six as they downed struggling Mainz 2-0 in Sinsheim.
Kevin Volland and Eugen Polanski netted the goals for Markus Gisdol’s men, who have slowly crept up on the top six and now have the chance of mixing with the likes of Schalke and Augsburg in the hunt for a place in Europe next season.
Mainz will now be looking over their shoulders again in the fight for survival after failing to build on their win from last weekend.
A last-gasp Salomon Kalou strike earned??Hertha Berlin??all three points and moved them out of the Bundesliga bottom three thanks to a 1-0 win over??Augsburg.
The Ivory Coast international grabbed the only goal of the game with just two minutes left on the clock to dent Augsburg’s hopes of qualifying for Europe next season and earn the Old Lady a precious victory.
Elsewhere, Eintracht Frankfurt bounced back from defeat to Mainz with Alexander Meier finding his scoring boots again in a 2-1 win over Hamburg.
Meier put Thomas Schaaf’s ahead through a 12th-minute penalty and, although Zoltan Stieber levelled on the stroke of half-time, Meier’s 16th of the season – one less than Bundesliga top scorer Arjen Robben – in the 54th minute earned the Eagles all three points.
Hamburg, who could slip back inside the bottom three on Sunday, also lost Matthias Ostrzolek to a red card, while Meier sent a second penalty against the crossbar at the death but it did not prove costly as Frankfurt edged to within four points of the top six.