The Bavarians raced into a three-goal lead after only 13 minutes, thanks to Mario Gomez, Franck Ribery and Bastian Schweinsteiger, and seemed on course to repeat their 7-0 hammering of Freiburg earlier this season.
However, they appeared to ease off after that, perhaps in view of Tuesday's Champions League clash with Napoli, with a second-half penalty from Gomez their only other addition.
And Heynckes admitted his side could easily have scored more than they did.
"We played economically," he told Sky television. "If we had wanted to step it up a bit then we would have been able to.
"That is a characteristic of my team that they can keep their concentration and win such games so comfortably."
Berlin coach Markus Babbel was grateful his former club showed him mercy, but admitted Bayern were simply in a different league to his side.
"That is high class and it is the best that German football has at the moment, and they belong among the best teams in Europe," he said.
"We have got to learn from games like this that we still have a long way to go to get to where they are.
"We showed too much respect and you cannot leave Bayern so much room or else you risk getting rolled over.
"Thank God that did not happen to us because I was definitely hoping they would not lead by so much at half-time.
"I think we still got away with it a bit only being 3-0 down."