A double from Sidney Sam saw Leverkusen move up to nine points with three wins in the league after the hosts had initially threw away a two-goal lead.
Nine-man Schalke 04, who have yet to win this season, slumped to their second defeat in three games with a 2-1 loss at Hanover 96 and with captain Benedikt Hoewedes sent off with a straight red card in the 14th minute.
Schalke, who drew 1-1 at home in the Champions League playoff first leg against Greece's PAOK in midweek, fell a goal behind after Szabolcs Huszti, who would later be sent off for a rough challenge, converted the spot kick after Hoewedes' foul in the box.
Mame Diouf doubled the lead for the hosts, drilling in a header from two metres before forward Adam Szalai cut the deficit. Schalke's Christian Fuchs was also sent off five minutes from time with a second booking to complete the visitors' misery.
Wolfsburg lost 2-0 at Mainz 05, another team with nine points, and also had new signing Luiz Gustavo sent off with a second booking in the 64th minute.
Hoffenheim had Sejad Salihovic sent off in the ninth minute of their 3-3 draw with Freiburg, who themselves had Francis Coquelin dismissed in the first half and Admir Mehmedi late in the second.