The Germany international broke the deadlock inside 20 minutes at Allianz Arena, smashing home the rebound after Robert Lewandowski's header was saved.
That goal was Muller's first in the Champions League this season, as he bids to enjoy a more productive campaign following his relatively barren 2016-17.
Muller scored just five Bundesliga goals, having plundered four times as many in the previous campaign, and Heynckes was happy to see the forward contributing as Bayern took control of second place in Group B following the 3-0 defeat to Paris Saint-Germain, a result that prompted the departure of Carlo Ancelotti.
"Well I think that the whole team have been really focused in every training session. There's a great atmosphere on the training ground. Something like that helps and motivates the players," Heynckes said.
"Thomas played in the same position on Saturday and played pretty well, but he's been working really hard. He not only scored the first goal, but he worked hard and ran a lot. He helped in defence as well.
"Today I saw the old Thomas Muller, the one that I know.
"But this is all necessary, especially from the well-established players and leaders in the team. He's the captain of the team so, of course, I'm happy about his form."