The deadlock was broken in just the 15th minute when Douglas Costa produced a moment of magic by cutting inside from the wing before finding the top corner with an unstoppable strike from 25 yards.
It could have been even worse for the hosts before the interval had Benaglio not made a fine save to keep out Muller after more good work from Costa on the wing.
An improvement from Wolfsburg did arrive after the break as Dieter Hecking's side started to enjoy more possession without ever threatening to spark an unlikely comeback.
Bayern were happy to settle for dictating the tempo for long spells, but poor defending almost cost them a clean sheet when Maximilian Arnold released Daniel Caligiuri, whose low effort was stopped by Manuel Neuer.
Wolfsburg finished a disappointing night strongly as Andre Schurrle collected an inch-perfect through-ball from Arnold before slotting past a helpless Neuer, but the consolation could not hide Bayern's superiority as Pep Guardiola's side booked their spot in the next round.