Croatia forward Mandzukic scored twice against his former team to take his tally to five after Bastian Schweinsteiger had given the hosts a 24th-minute lead in an impressive display of attacking football by the Bavarians, who have 15 points.
Second-placed Eintracht Frankfurt came back twice, including from two goals down, to earn a 3-3 draw at home to champions Borussia Dortmund, who dropped to fifth place on eight points.
"Although we dominated throughout, Wolfsburg were not an easy opponent," Bayern coach Jupp Heynckes told reporters.
"We failed to add another after our 1-0 lead despite the number of good chances. It was only settled after we scored to go 2-0 up."
Wolfsburg's Ricardo Rodriguez almost snatched a surprise equaliser against the run of play but his powerful shot from a tight angle scraped the post from their only real chance.
Dortmund, struggling to find consistency this term, failed to bounce back from Saturday's 3-2 loss at Hamburg, squandering a two-goal first half lead as Frankfurt scored in the 49th and 51st minute with Stefan Aigner and Japanese Takashi Inui.
Substitute Mario Goetze put them back in front three minutes later from close range but surprise package Frankfurt, who won their first four games, rallied again through Bamba Anderson's header midway through the second half to rescue a point.
"That was the best performance I have seen from a Frankfurt team," said Dortmund coach Jurgen Klopp. "They have had many good teams in the past but this was top quality."
