"It was a hard-fought victory against a very good team," Heynckes told Bayern's official website. "We didn't look determined enough, particularly in the first half, and Frankfurt played good football and were full of running.
"It's hard to re-focus after the Champions League. You can't always score six goals and play superb football. But we showed that we're capable of the right reaction in a difficult situation.
"In that sense, the team were excellent. We made the most of our experience and intelligence."
Bayern are currently at the top of the Bundesliga table with 30 points from 11 matches.