Diego Klimowicz gave the visitors the lead in the 32nd minute after just beating defender Manuel Friedrich to the ball, but Friedrich equalized three minutes from the break with a header.
German international Stefan Kiessling scored the winner for his side in the 68th minute after being set up by Toni Kroos. It was Kiessling's fourth goal of the season and sees him top the scorer charts.
The striker said that they had dominated the game. 'Last week we made many goals out of few chances, today we made few goals out of many chances.
'It is looking really good for us at the moment and we need to now follow up with other wins,' he said.
Schalke 04 missed an opportunity to join Leverkusen at the top when they slumped to a 1-0 defeat at home against SC Freiburg, with South Korean defender Du-Ri Cha scoring the only goal of the game five minutes from the break.
Schalke coach Felix Magath, who lost his first game in charge of the team, said that his team simply did not do enough.
'We were headless and without a plan. I have no idea who told the players that they could only play high balls into the area. That is what they did,' he said.
In other matches Brazilian midfielder Carlos Eduardo scored the only goal of the game as Hoffenheim secured their first three-pointer of the season with a 1-0 victory at struggling Hanover 96, while VfB Stuttgart and Nuremberg played to a goalless draw.
Nuremberg remain one of two Bundesliga clubs to have not yet won a match this season, with the other club - Cologne - still to play their fourth game.
In Frankfurt Eintracht Frankfurt and Borussia Dortmund shared the spoils in a 1-1 draw.
Egyptian international Mohamed Zidan gave the visitors the lead on the hour, but Greek striker Ioannis Amanatidis found a well-deserved equaliser in the 68th minute.