The Bavarians have stuttered slightly in the opening weeks of 2013, with the announcement of Pep Guardiola's impending arrival and a post-winter break rustiness appearing to play their respective parts.
But goals from Thomas Muller and Mario Mandzukic gave FCB a comfortable win on Sunday and increased their lead at the top of the Bundesliga to 11 points, to leave Heynckes a satisfied man.
"We were significantly better than against Furth. My team were very composed for the entire 90 minutes and totally focused right from the first whistle," he told reporters after the game.
"Our shape and organisation were excellent, our movement was tactically very good and we afforded [Stuttgart] almost nothing in attack. But in the first half, we just lacked a little flair, determination and urgency."
Despite his contentment with his side's efforts, Heynckes revealed that a fiery half-time team talk was needed to extract the best from his players.
He added: "We failed to find the final pass, cross or shot at goal. I complained about that at half-time and we were much better in the second period.
"Stuttgart pulled everyone back so it was never easy, but that's when you have to raise your game, which is what we did in the second half. Ultimately, you force your opponents into errors."
Bayern's next opponents are Mainz next Saturday.