Lewandowski moved to Bayern from Dortmund in the close-season, and marked his first league return to Signal Iduna Park with the decisive goal in the 36th minute.
The Poland international reacted quickest to a rebound after Roman Weidenfeller parried Thomas Muller's initial shot, nodding into the unguarded net.
It was his second in as many Bundesliga outings against Dortmund after his effort in the 2-1 win back in November, and victory keeps Bayern 10 points clear at the top of the table.
Behind Bayern, the rest of the top four all enjoyed comfortable victories to further cement their places as the Bundesliga's likely UEFA Champions League representatives next season.
Wolfsburg defeated Stuttgart 3-1 at home, thanks to a brace from Ricardo Rodriguez and Andre Schurrle's first goal for the club.
They remain seven points clear of Borussia Monchengladbach, who thumped Hoffenheim 4-1 away from home.
Patrick Herrmann, who earlier this week extended his contract at the club until 2019, scored twice as the visitors came from behind, with Max Kruse and Raffael also netting.
Gonzalo Castro and Stefan Kiessling each netted braces in Bayer Leverkusen's 4-0 thrashing of struggling Hamburg, while Mike Frantz's goal earned Freiburg a 1-0 victory over Cologne.
Elsewhere, Hannover benefited from a goal off Marcelo's backside as they came from two down to draw 2-2 at Eintracht Frankfurt and the game between Werder Bremen and Mainz ended goalless.
