Leverkusen won 2-0 at bottom side Darmstadt on Saturday while Bayern's 3-1 over Borussia Monchengladbach was made extra special as it marked Thomas Muller's 500th career victory for them.
Nathan Tella scored a 33rd and 52nd minute brace as Leverkusen regrouped well from a 0-0 draw against Gladbach eight days ago to remain unbeaten in all competitions.
Gladbach led in Munich from Nico Elvedi in the 35th minute but the champions fought back from teenager Aleksandar Pavlovic in the 45th, the league's top scorer Harry Kane in the 70th and Matthijs de Ligt in the 86th.
Club icon Muller was involved in Bayern's first and second goals en route to becoming their first player to win 500 official games.
"I am not really a friend of these anniversaries but the team gave a shirt and celebrated me," Muller told Sky TV.
"The best thing is the feeling of winning. I think we are also on a good path to win in Leverkusen."
The leaders had a hard time at first against a well-organised Darmstadt defence before Tella broke the deadlock in the 33rd when he headed home Alejandro Grimaldo's cross from the left at the far post.
Tella struck again seven minutes after the restart from a right angle, set up nicely by Germany player Florian Wirtz.
In Munich, Leroy Sane hit the crossbar in the fifth minute but Gladbach took a 35th-minute lead with the help of Bayern keeper Manuel Neuer whose pass to Muller was intercepted by Elvedi who then got the ball back and slotted into the bottom right corner.
Bayern were quickly level from Pavlovic after being set up by Müller. Kane then headed into the empty net in the 70th for his 24th goal of the season after goalkeeper Moritz Nicolas had failed to reach a cross, under pressure from Muller.
Stuttgart had a dream start in Freiburg with two goals in the first seven minutes from Deniz Undav's 13th goal of the season and Chris Fuhrich.
Freiburg's Merlin Rohl was sent off in the 18th minute for a reckless challenge on Maximilian Mittelstädt.
The hosts pulled one back late in the half from Lukas Kubler but Mittelstadt's third in the 74th decided a game interrupted in both halfs when fans threw chocolate coins and other objects onto the pitch in ongoing protests against external investors for the German Football League.