Brazilian defender Lucio gave Leverkusen the lead after just nine minutes but Thomas Brdaric was then sent off for his second yellow card after just 37 minutes.
Despite being up against the odds the hosts doubled their advantage just after the hour mark through Daniel Bierofka and held on for the win despite Hasan Salihamidzic grabbing a late goal two minutes from the end.
Armeinia Bielefield also recorded an impressive 2-1 home win against Schalke despite playing the last half an hour with ten men.
Erhan Albayrak grabbed an early penalty for the hosts only for Gustavo Varela to score a penalty of his own for Schalke.
Artur Wichniarek was then dismissed in the 56th minute but it was the ten men who went to to grab the winner through Mamadou Diabang.
Borussia Dortmund left it late at home to Borussia Monchengladbach as Ewerthon grabbed the only goal of the game in the 85th minute.
Tomislav Maric scored to hand Wolfsburg a 1-0 win away at Energie Cottbus while Markus Schroth did the same for Munich 1860 against Hertha Berlin.
Hamburg eventually overcame Stuttgart to secure a 3-2 home win while the other game of the day saw Hannover earn a 2-1 win at Hansa Rostock.
Click below for match summaries:
1860 v Hertha Berlin
Arminia Bielefeld v Schalke
Bayer Leverkusen v Bayern Munich
Borussia Dortmund v Borussia Monchengladbach
Energie Cottbus v Wolfsburg
Hamburg v Stuttgart
Hansa Rostock v Hannover
