The Bavarians maintained their 100% winning start to the season as former Wolves striker Mario Mandzukic returned to haunt his former club with two headed goals after the interval following Bastian Schweinsteiger's first-half opener.
While Heynckes paid tribute to last night's opponents, the veteran coach expressed frustration for his side's failure to kill the game off sooner.
"It wasn't as easy as the result and the number of chances would suggest. We were up for it physically and allowed them very few chances," said the 67-year-old.
"After we took the lead, we had any number of excellent chances but failed to score a second. Despite our dominance, it wasn't easy against Wolfsburg, but once we'd gone 2-0 up, you could see it was done and dusted, and our opponents recognised they wouldn't take anything away from here.
"We could definitely have scored more goals."
Bayern moved two points clear at the top of the Bundesliga following their fifth successive victory - seven in all competitions.
And striker Mandzukic has put their early success down to strong team unity.
"You can see we're all enjoying it," said the Croatia international.
"Every one of us is fighting for the others out on the field, and that's how we want to carry on. I'm enjoying every day with this team."
Wolfsburg have just one win from their opening five league games and boss Felix Magath, who guided Bayern to two consecutive league and cup doubles in 2005 and 2006, was left to reflect on a humbling defeat.
"I'd hoped Bayern might not take us seriously after all their recent good performances. But my hopes were dashed straight away," he said.
"Bayern immediately put us under pressure and played good football. We have to accept that Bayern are too good for us at the moment."