Dortmund are on 51 points, more than any team in second place has ever had after 22 matches, but they are still eight behind the Bavarians, who won 3-1 against Darmstadt 98 on Saturday.
Dortmund, who have more points after 22 matchdays than 42 of the 52 Bundesliga champions had at that stage, are a massive 15 points clear of third-placed Hertha Berlin, who have 36.
It took them almost 45 minutes, however, to create a decent chance with Aubameyang firing wide from a good position.
News that makes sense
Your trusted source for staying up-to-date with the world around you. Get free daily news updates and analysis, straight to your inbox.
Leverkusen responded with a chance of their own but Karim Bellarabi's shot was palmed wide by keeper Roman Buerki.
African player of the year Aubameyang struck in the 64th minute with Erik Durm delivering a fine cutback and the Gabon international tapping in for his 21st league goal this season.
The goal prompted an angry reaction from Leverkusen coach Roger Schmidt, who was sent to the stands by the referee, but refused to leave his technical area, causing the game to be briefly interrupted.
Referee Felix Zwayer stopped play and left the pitch until Schmidt followed his orders.
Leverkusen's Javier Hernandez should have grabbed an equaliser for the hosts in the 90th minute but the Mexican forward shot wide from close range with only the keeper to beat.
(Reporting by Karolos Grohmann; editing by Toby Davis)
