
Bayern captain Muller put the hosts ahead after 17 minutes before goals by Joshua Kimmich and Mats Hummels sealed the victory on Wednesday at the Allianz Arena.
The result leaves Bayern second in Group B on six points, three behind leaders Paris Saint-Germain and three clear of third-placed Celtic.
It was an important result for Bayern in the wake of their 3-0 drubbing in Paris three weeks ago, which led to Carlo Ancelotti's dismissal.
Heynckes, 72, came out of a four-year retirement for his fourth stint as Bayern coach to replace Ancelotti.
He restored Muller to his preferred attacking midfield role, allowing him to happily roam just behind Robert Lewandowski, with Thiago Alcantara dropping into a deeper position.
"Thomas put in a good performance, he ran a lot, was very present and we saw the old Thomas Muller," said Heynckes. "He's an established player, the captain and it's good to see him playing well again."
Muller struggled for form under Ancelotti and was often played out of position.
But while the Germany star was delighted to see Bayern pick up the three points in Europe and build on Saturday's 5-0 thumping of Freiburg in the Bundesliga, he said there is room for improvement in their finishing.
"The attitude was better, we were motivated after the win at Freiburg and wanted to use the momentum," said Muller. "That was an important three points. We created a lot of chances in the second half which we should have used."
Heynckes was also unhappy with Bayern's finishing — pointing to the 29 shots on goal which yielded only the three goals.
"We created a lot of chances that we didn't take advantage of and, at the other end, let them have a few themselves," said Heynckes. "We were a bit negligent there and we cannot let that happen. You need to be completely alert from the first to last minute."
The trio of James Rodriguez, Arturo Vidal and Corentin Tolisso, Bayern's record signing, all started on the bench, but Heynckes said they will get their chances.
"It's necessary to develop momentum and win the first few games, either in the Bundesliga or Champions League," said Heynckes. "For that reason, we cannot afford to experiment much with new players. But I spoke to all the players that weren't involved to ensure them that they do have a role in the team, especially with a busy schedule coming up."
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