The Bavarian giants racked up a record 16th straight Bundesliga victory at the Volkswagen Arena, and opened up a 23-point gap at the top of the table.
Things started badly for the visitors, however, as Naldo volleyed home Kevin De Bruyne's teasing cross.
Xherdan Shaqiri ensured the sides went in level at the break, however, before two goals apiece from Thomas Muller and Mario Mandzukic, as well as a strike from Franck Ribery on his comeback from injury, saw Bayern rack up four or more goals in their fourth straight league match.
Despite the ease with which Bayern eventually collected three points, Guardiola was not fully satisfied with their performance.
Speaking to the club's official website, he said: "We were not as dominant as in recent games.
"Wolfsburg had super organisation and were very aggressive.
"In the first half we had problems, even in the first 15 minutes of the second half. But at the end of we have scored the goals."
