The 67-year-old boss allows his side a momentary blip with a shaky cup performance, but insists that overall he is extremely satisfied with his squad's progress this season
Goals from Mario Gomez and Xherdan Shaqiri either side of half time wrapped up the win for the Bundesliga leaders, despite Bayern going down to 10 men.
"We knew it would be extremely tough," Heynckes told the club's official website.
"It's the last match of the year. The players have already moved on mentally.
"We didn't play well in the first half. In particular, our switching from defence to attack malfunctioned. We've had a lot of matches so far this season, and you have to accept you'll have an off day."
Despite Franck Ribery picking up a red card in the 47th minute for slapping Ja-Cheol Koo, Bayern were able to close out the victory, but Heynckes remained critical of Ribery's reaction despite winning the match.
"The red card was the result of provocation, but there's no disputing the decision. FC Bayern players have to brush that kind of thing off.
"We were much better in defence after the substitutions, and I knew we'd always be a threat on the break.
"Overall I'm very satisfied, because we've been outstanding for long periods in the first half of the season. It can't go better than this," he said.