Bayern caused some early problems for Wolfsburg, hitting the woodwork and forcing the goalkeeper into two saves inside the first seven minutes.
In the 20th minute, they made their dominance count when Leon Goretzka took on a simple pass from Joshua Kimmich and sent it flying into the net from outside the box.
Wolfsburg had shown they had some fight in them, though, and pulled level with a fantastic routine from a free-kick that resulted in a lovely finish from Mohamed Amoura in the 24th minute.
The home side had a tough time finding their way through Wolfsburg's defence after that, but the visitors couldn't stop Michael Olise as he pounced on a loose ball, evaded a challenge outside the box and fired towards goal, finding the net despite Kamil Grabara getting a hand to it.
Just before half-time, the Bavarian giants thought they had a two-goal cushion when Joshua Kimmich diverted in from Kingsley Coman's cross, but a VAR review showed it struck his arm and it was disallowed.
Their inevitable third goal came just after the hour mark, again Goretzka getting in the air to meet Olise's free-kick cross and divert home. A few minutes later, a long Manuel Neuer ball caused a mix-up in the Wolfsburg defence, allowing Coman to go through on goal, but his shot missed the target.
The hosts were in for a difficult end when Wolfsburg won the ball in the middle of the field and Tiago Tomas drove forward with determination before feeding through Amoura for an excellent strike to make it 3-2 after 88 minutes. In the end, though, Bayern held on to the lead and sealed the three points.