Former Bayern striker Ivica Olic replied for Wolfsburg after Thomas Muller and Arjen Robben had given the champions a two-goal lead, but Pep Guardiola's side hung on to begin their season with three points.
The Wolfsburg keeper had earlier denied Lewandowski in a one-on-one situation, but was beaten on 37 minutes when Robben dribbled to the byline before squaring for Muller to convert from close range.
It took just two minutes of the second period for Bayern to increase their lead as Robben added his own name to the scoresheet by finishing off a quick break which he started on the halfway line.
The visitors reduced the arrears on 52 minutes when Olic ran away from Holger Badstuber, who was making his first appearance since December 2012, before chipping Manuel Neuer from the edge of the box.
Munich nearly made the final few minutes more comfortable when Sebastian Rode found the net, but his effort was ruled out for offside, with Muller adjudged to be interfering with play as he ran in front of the goalkeeper.