Heynckes rotated his side considerably with qualification for the knockout stage already in the bag, but there was still a job to be done in clinching top spot and his team obliged in style.
"Of course I am very satisfied," said Heynckes. "It was our primary goal to win and to top the group.
"This newly-formed team played an engaged and alert game. We hardly let anything through in defence.
"It was a dominant performance overall and congratulations go to my team."
Finishing top of Group F means Bayern will be seeded in the draw on December 20, but Heynckes says the only advantage of that is being able to play at home in the second leg.
"There's no easy game in the Champions League," he added on his club's website. "The teams who finish second in the group are also very strong."
Last year's beaten finalists therefore have no particular preference for their next opponent, according to striker Mario Gomez.
"We just take what comes," said the Germany striker. "We want to go as far as possible, preferably right through to the final.
"That means we have to beat every opponent so we'll just see who we get in the draw."