A single change from Bayern saw Jamal Musiala introduced for Kingsley Coman following elimination to Paris Saint-Germain in the UEFA Champions League on Tuesday.
Musiala made his presence felt instantaneously inside 15 minutes after he beat Maxence Lacroix in a one-on-one challenge before going on to find the near post from inside the six-yard area.
Bayern claimed a second just inside six minutes from the half-hour mark as a handling error from goalkeeper Koen Casteels gave Eric Maxim Choupo-Moting the easiest of finishes from close-range.
Wolfsburg pulled a goal back ten minutes to halftime from a curling strike from 12 yards out by Wout Weghorst following a well-worked cutback from Xaver Schlager.
The champions though restored their two-goal cushion after two minutes when Musiala rose at the back-post to head a pin-point cross from Thomas Muller home.
Hansi Flick's side remained nervous following nine minutes from the break and conceded a second after Maximilian Phillip beat Manuel Neuer to a delivery to convert from close-range.
A substitution followed the host a minute later in Josip Brekalo, who made an entry ahead of Ridle Baku with the balance of play well poised.
Bayern maintained calm and managed to carve out promising chances in the closing quarter, but Leroy Sane in particular failed to pounce.
However, Wolfsburg could've stolen the equaliser through a snap effort from Weghorst moments afterwards but Neuer parried as the defence battled.
Chances continued to fall either way inside the final minutes, but Bayern took charge to confirm victory and go seven points clear at the top of the table.