The Croatia international enjoyed a happy return to the club he left last summer, as he scored a fantastic goal, with the Netherlands winger adding the clincher
Despite the unremarkable margin of victory, Bayern was always in control but, perhaps with next week's Champions League trip to Arsenal on the agenda, never looked to overexert itself against a side with one of the worst home records in the division.
Mario Mandzukic showed no mercy against his former club when firing home a fantastic overhead effort in the first half, with Arjen Robben rounding off matters emphatically in injury-time to provisionally send the visitors 18 points clear of Borussia Dortmund at the top of the Bundesliga.
Jupp Heynckes was spoiled for choice when naming his starting lineup, and fielded a side with little surprises, with Robben and Jerome Boateng again taking their places on the bench.
Bayern typically dominated possession throughout the first half, but despite some promising build-up play, the final ball was lacking, breaking down a number of their attacks.
Wolfsburg was diligent in defense, and through the pace and directness of Marcel Schafer and Ivica Olic, found themselves with a purposeful outlet on the left flank to relieve pressure on their goal.
The first half seemed destined to end in a stalemate, but, nine minutes before the break, a moment of magic from Mandzukic broke the deadlock in stunning fashion.
Toni Kroos pumped a free kick towards the far post, and Bastian Schweinsteiger nodded back to the Croatia striker, who connected superbly with an overhead kick that rifled in from 15 yards out.
The home side made an improved effort to get themselves back into the game in the second half, but were still indebted to Naldo for hacking clear a goalbound Thomas Muller effort off the line.
Vieirinha blasted off target from 20 yards out, but Wolfsburg’s best chance of the match came from Diego, who bent a free kick towards the corner that brought the best out of Manuel Neuer with a quarter of an hour to go.
But the hosts' eagerness to get back into the match would cost them at the death, as Muller found Robben peeling away in space, and the winger buried a powerful low finish to seal the game.
With the victory secure, Bayern can now focus all its attention on the club's visit to to Arsenal next Wednesday, while Wolfsburg's next action is a league encounter at Mainz on Sunday.