Goals from Javi Martinez and Franck Ribery put Bayern in complete control and James Rodriguez's sublime free-kick helped secure the points after Kevin Volland's deflected strike had given Leverkusen hope.
"After the 2-0 we lost a bit of our concentration and had unforced errors with the ball".
"It will be tough at Leverkusen and we will have to give our all to win there", said the Frenchman.
Heynckes, 72, coached Leverkusen between 2009 and 2011 and was under no illusions about the hard task presented by his former side, who are buoyed by a 12-game unbeaten run in all competitions which has seen them rise to fourth in the table.
But the 73-year-old Heynckes, who has already been coaxed out of retirement, has always maintained that he was stepping in as a favor during a hard time, and that he will not be staying on beyond the end of the season.More news: Illinois AG candidate robbed at gunpoint in Chicago during campaign photoshoot
"I don't think it changes that much [about how they play]", the Bayern boss said.
Goalkeeper Sven Ulreich, who will again deputise for the injured Manuel Neuer, added: "They're risky opponents who break forward quickly".
The visitors took the lead in the 32nd minute when Martinez fired in from close range after Leverkusen failed to clear an Arturo Vidal header.More news: Dissidia Final Fantasy NT Open Beta Begins
In Hummels' absence, Heynckes will most likely pair Niklas Suele and Jerome Boateng at centre-back.
Leverkusen lacked in clear-cut chances in the first half but after the restart Leon Bailey nearly levelled the scores but his effort rattled only the bar with 54 minutes played.
The 20-year-old showed a glimpse of his talent by cutting in from the right, beating two players and clipped the crossbar with his shot.
Just when the hosts were on the front foot, Bayern doubled the scores out of the blue as Rodriguez passed into the path of Franck Ribery, who had all time and space to place the ball into the bottom near corner in the 59th minute.
However, the goal sparked Leverkusen into life.More news: Can Tom Brady Escape His Struggles-and Other Key NFL Playoff Questions
Another chance presented itself to Volland late on, as Kai Havertz fed the striker into the penalty area, but his first touch was poor and allowed Ulreich to make a vital save.