Bayern clocked up a 10th successive Bundesliga win despite falling behind to an early Daniel Didavi goal and missing a penalty when Arjen Robben's effort was saved by Koen Casteels just after halftime.
The victor came in the 91st minute from the spot thanks to Lewandowski, after Robben had seen an earlier penalty saved.
Muller's introduction in the 62nd minute proved a big turning point in the contest, and Heynckes says the Germany forward was key to Bayern's triumph.
"After the early opener Wolfsburg set up their game with a compact defence", said the 72-year-old on the Bayern website.
Rudy spurned two good opportunities as Bayern's frustrations started to show with Thiago, who replaced the suspended Arturo Vidal for his first start in three months due to a thigh injury, and Franck Ribery both receiving yellow cards for cynical fouls as Heynckes' men registered just one shot on target in a tepid first-half showing.
"We dominated possession but failed to play vertically".
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"I knew we wouldn't score this way".
"During the second half we played more fluently and faster, and we are happy".
Wolfsburg's hardcore fans missed it, however, as they were outside protesting against the management of the club, founded in 1945, and had refused to enter the stadium until after 19 minutes and 45 seconds.
Wolfsburg boss Martin Schmidt, meanwhile, lamented the lack of a clinical edge to his side's display.
"That's a real shame, because we had a set plan for where the ball should go. That's how the game eventually got away from us - it was too little to earn a win".
While Wolfsburg will now switch focus to their clash with fellow strugglers Mainz, Heynckes and Bayern turn their attention to the Champions League round of 16 clash with Besiktas in midweek.