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.
"We lost our concentration a bit after leading 2-0 but it is just hard to win here". Bayern are comfortable atop the table, 11 points clear of second-place Schalke and 13 points ahead of fourth-place Bayer Leverkusen.
The winter break in Germany is over, and once again we find ourselves with Bayern Munich already threatening to pull away from the rest of the Bundesliga with the season just half over.
"I have said everything there is to say and won't say anything more", replied Heynckes when asked about his future in the midst of Bayern's hunt for a new head coach for 2018/19.
The Poland star is returning to full training after a knee injury, but Heynckes opted to start Thomas Mueller up front for Bayern.
Munich-conceived Wagner joined Bayern at nine years old, making his Bundesliga make a big appearance in 2007 yet neglected to make the leap forward, showing up before moving to Duisburg the next year.
While goalkeeper Manuel Neuer is still recovering from a fractured foot, Mueller wore the captain's armband and Sven Ulreich was in Bayern's goal.
In Hummels' absence, Heynckes will most likely pair Niklas Suele and Jerome Boateng at centre-back.
And Bayern punished his profligacy in the 32nd minute - Martinez blasting in from close range after Vidal's header ricocheted into his path.
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 has scored six goals and assisted on four others.
He dribbled his way through the defence then unleashed a thunderbolt of a shot which gave Leverkusen's Germany goalkeeper Bernd Leno no chance.
Ribery then made sure of the three points on 59 minutes in emphatic style.
Leverkusen warmed up for Bayern with a 2-2 draw in a friendly against third-tier Preussen Muenster as Argentina striker Lucas Alario netted both goals following his recovery from a groin injury.