After the midfielder had put die Roten ahead, the Croatian striker netted two second-half headers to secure his side all three points with a resounding victory
The result never looked in doubt for the hosts as Bastian Schweinsteiger hit the woodwork twice before finally putting his side ahead in the 24th minute. Jupp Heynckes' men dominated in the wide areas from then on but it was not until the second half that a Mario Mandzukic brace provided the gloss to the scoreline.
As we have come to expect from Bayern this season, they started at an electric pace and should well have been ahead after just three minutes. Dante's header from a corner fell at the feet of Schweinsteiger inside the six-yard box but the midfielder somehow failed to convert and only rattled the post.
Wolfsburg were shocked and started to flood men behind the ball when not in possession but with space limited, Heynckes' side decided to try their luck from distance.
It was Schweinsteiger again who had Diego Benaglio worried with a venomous 30-yard strike, but once again his effort crashed off the frame of the goal.
But the third time proved to be the charm for Schweinsteiger in the 25th minute. Arjen Robben played Franck Ribery in on the right and his cutback was swept between the legs of Benaglio by the Germany international.
Die Roten became guilty of easing off but with Ribery tearing down the left they still had chances to increase their lead before the break. But they were halted in their tracks by Benaglio as he clawed a Mandzukic effort wide of the post before parrying an attempt from Robben behind on the stroke of half time.
Bayern began the second half just as they did the first, forcing the visitors onto the back foot with rapid attacking play. This time though it took just two minutes to threaten the Wolfsburg goal but Benaglio refused to be beaten again with a solid double-save from Ribery and then Robben.
Again, the Wolves were unable to hold out and the hosts doubled their lead in the 58th minute. Xherdan Shaqiri surged forward down the left, turning Naldo inside out before crossing to the back post. Mandzukic was there and he rose above a weak challenge from Ricardo Rodriguez to nod into the back of the net.
Bayern added a third just eight minutes later as Wolfsburg's defensive woes mounted. Philipp Lahm was given too much space by Rodriguez and the full-back's cross was diverted into the back of the net by Mandzukic for his fifth of the season.
The hosts could finally feel comfortable with their three-goal cushion and they saw the remainder of the game out with minimal threat.
The three points mean Bayern have won all five of their opening league fixtures and following Eintracht Frankfurt's 3-3 draw with Borussia Dortmund, they open up a two-point lead at the summit.