The league leaders converted their only shot on target at the Commerzbank-Arena as Arturo Vidal headed home Joshua Kimmich's pinpoint cross after 20 minutes.
Bayern's surprise lack of creativity in the final third mattered little, though, as they comfortably kept Frankfurt at bay, easing to a seventh league win since Heynckes' return.
"I think the autumn championship is not so important," he told Sky.
"What matters is that we won and we were able to extend our lead.
"It was an uncomfortable game against an uncomfortable opponent. The table makes us happy."
For Frankfurt boss Niko Kovac, there was disappointment after a disciplined display ended in defeat against illustrious opponents.
"My team has played a really good game," he told a news conference. "We gave everything from the first to the last minute. We deserved more than defeat.
"We showed that we can compete. That's why we look ahead. The only difference [between the sides] was that Bayern scored from their only chance. We never gave up, that's why I am very positive.
"We will continue to work hard and hope to have a little bit of luck back on our side in the future."