The win moved Bayern seven points clear at the top of the Bundesliga table.
Jamal Musiala and Eric Maxim Choupo-Moting put Bayern 2-0 up early on.
Wout Weghorst pulled a goal back only for Musiala to net again, and Bayern held on despite Maximilian Philipp’s sweet second-half half-volley.
After second-placed RB Leipzig drew 0-0 with Hoffenheim on Friday night, Bayern’s win could prove decisive in the title race with just five games remaining.
Bayern keeper Manuel Neuer crucially denied Weghorst an equaliser with a smart save in the 66th minute.
The Wolfsburg striker had been flagged offside but replays suggested that decision would have been overturned by the video assistant referee had his finish beaten Neuer.
Seventeen-year-old Musiala, who earlier this season opted to play international football for Germany over England and Nigeria, had an effort cleared off the line in the second half as he chased a hat-trick.