Lewandowski confirmed earlier this week that he will sign a pre-contract agreement with Bayern Munich in January, but he was named in Dortmund's starting line-up on Saturday and struck twice in the second half.
The visitors already led 2-0 through Marco Reus' brace, the second a penalty after Fallou Diagne was sent off for fouling Lewandowski, and substitute Jakub Blaszczykowski completed a thoroughly one-sided win.
Dortmund remain level on points with Bayern Munich at the summit after the reigning champions beat Wolfsburg 1-0.
Thomas Muller struck the only goal from a narrow angle in the 63rd minute and Bayern, like their rivals, moved to 19 points from seven games in an unbeaten start.
Just one point behind are Bayer Leverkusen, who extended their best-ever start to a Bundesliga season with a 2-0 win over Hannover at the BayArena.
Simon Rolfes and Sidney Sam scored first-half goals as Leverkusen warmed up for their midweek Champions League tie with Real Sociedad with their sixth win in seven league matches this season.
The win also gives Sami Hyypia's men a six-point cushion over Hannover, who remain in fourth place despite losing their third way game of the season.
Hoffenheim and Schalke drew 3-3 in a dramatic game at the Rhein-Neckar Arena.
Kevin-Prince Boateng and Joel Matip got Schalke off to a flying start, but Anthony Modeste hauled Hoffenheim back into the game.
Marco Hoger restored Schalke's two-goal advantage before half time, but a Roberto Firmino penalty and a David Abraham free-kick earned Hoffenheim a share of the spoils.
Hertha Berlin came from behind to beat Mainz 3-1 at the Olympiastadion and move up to fifth in the table.
Nicolai Muller gave Mainz a seventh-minute lead, but their former striker Sami Allagui came back to haunt them with two goals to turn the game on its head and Anis Ben-Hatira completed the win for Hertha.
Hamburg twice came from behind to draw 2-2 at Eintracht Frankfurt in the late kick-off.
Johannes Flum and Marco Russ each gave Eintracht the lead, but Hamburg's equalisers came from Pierre-Michel Lasogga in first-half stoppage time and Marcell Jansen in the 86th minute.