Japanese star Shinji Kagawa got the scoring underway and
gave Dortmund the lead from close range on 25 minutes, and both Christian Pulisic and Andriy Yarmolenko had chances to double the advantage before half-time.
With just over an hour played, Yarmolenko surged forward on the counter attack to set up a goal for Pierre-Emerick Aubameyang.
Beating Dortmund ‘massive’ for confidence: Pochettino
The Gabonese striker tapped the ball in from less than a metre in front of goal, scoring his fourth and no doubt easiest goal of the season so far.
American international Pulisic secured victory in the 80th minute, netting Dortmund's third from inside the penalty area.
Dortmund, who have yet to concede a goal in five games this season, are now a point clear of Bayern Munich, who remain second after surprise package Hanover failed to win in Freiburg.
Loew’s Germany ready to enter World Cup on high
The promoted side remain unbeaten this season, but were denied the opportunity to leapfrog Bayern by a late Nils Petersen equaliser.
After Florian Niederlechner had missed a penalty for Freiburg early in the second half, Martin Harnik gave Hanover the lead in the 66th minute. Petersen's close range effort saved a point for the home side with seven minutes to play.
Hanover now drop to fourth after an injury time goal from Mark Uth saw Hoffenheim beat Mainz 3-2 despite trailing 2-0 early in the game.
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