The win at the Volkswagen Arena means that the Bavarian giants are 18 points clear at the top of the table at the moment.
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Bayern were in control of the match right from the start and could have surged ahead as early as the third minute.
Mandzukic created space on the right for a cross to set up Thomas Muller, whose downward header went wide.
The contest became more even thereafter, with no clear-cut chances being crafted by either side.
Then Bayern pulled ahead in the 36th minute thanks to an acrobatic effort from Mandzukic, who turned in Bastian Schweinsteiger's pass with an overhead kick.
Muller could have doubled his side's advantage in the opening minutes of the second half, but for a good intervention from Naldo inside the Wolfsburg penalty box. Minutes later the Germany international's shot was blocked by Alexander Madlung.
Wolfsburg lacked any incisiveness to penetrate Bayern's defence, although Diego did have a good chance to restore parity after 77 minutes.
However, the Brazilian playmaker's curling free kick from 25 yards was smartly kept out by Manuel Neuer.
Bayern wrapped up the points in the second minute of injury time when Arjen Robben finished emphatically after latching on to Muller's pass.