Dortmund manager Edin Terzic praised his team's defence in the "fair result", but hit out at VAR, who declined to intervene despite what seemed like a late foul on winger Karim Adeyemi.
Although only two points ahead of a Harry Kane-powered Bayern Munich, Leverkusen are already a whopping ten points in front of Borussia Dortmund.
Bayer Leverkusen have won 17 and drawn one of their 18 fixtures in all competitions this season.
With 31 of a possible 33 points from 11 games, Bayer Leverkusen have equalled the greatest start in Bundesliga history.
With 16 wins and a draw in 17 matches in all competitions, Xabi Alonso's Bayer Leverkusen could scarcely have had a better start to the season.
The victory means Leverkusen have amassed 31 of a possible 33 points after 11 matches, equal to the record set by Pep Guardiola's Bayern Munich in 2015-16.
Bayer Leverkusen only dropped points against Bayern, with the sides playing out a pulsating 2-2 draw in Munich in September.
Harry Kane scored a hat-trick as Bayern Munich thrashed Borussia Dortmund 4-0 away on Saturday
Bayern Munich were beaten by Holstein Kiel on penalties at the same stage three years ago.
Harry Kane scored his ninth goal in eight league matches as Bayern Munich won 3-1 at Mainz on Saturday
Xabi Alonso's Bayer Leverkusen are dreaming of a Bundesliga title challenge, just a year since the Spaniard took over as coach
Bayern Munich came back from two goals down to draw 2-2 at RB Leipzig on Saturday as Harry Kane kick-started a second-half revival to prevent a first league loss of the season.
Harry Kane's fourth goal in four Bundesliga games was not enough as Bayern Munich were held to a 2-2 home draw by Bayer Leverkusen on Friday
Iran forward Sardar Azmoun signed for Roma on loan from Bayer Leverkusen on Saturday as the Serie A club tries to hammer out a deal to take Romelu Lukaku from Chelsea.
Jose Mourinho's Roma remain on track for a second European trophy in two seasons after a goalless draw at Bayer Leverkusen.
Leverkusen's revival from the relegation spots to European trophy candidates under Alonso has been driven by the side's youthful array of attacking talent.
Bayer Leverkusen end the round in seventh on goal difference, with sixth place qualifying for the Europa Conference League.
Roma took the win despite having a host of players either out or barely fit to play, with stars Paulo Dybala and Georginio Wijnaldum only coming on in the final 15 minutes.