The Bavarians kicked off 2018 with a potential banana skin but demonstrated their class as goals from Javi Martinez, Franck Ribery and James Rodriguez saw them overcome a side who had not lost in their previous 12 Bundesliga games.
However, Bayern were in control throughout and that particularly pleased their veteran coach as they march on towards a sixth successive league title.
Ribery's second-half strike was his first of the campaign, and the Frenchman was delighted to have had an impact for the leaders on a tough away trip. "We are relaxed. The only club that can say no - and would do so - if a player attracted interest is Bayern Munich", Voller said in an interview with Die Welt. - Wendell played in his 100th Bundesliga game and became the fifth Brazilian to do so for Leverkusen. But after working hard in Qatar [during a mid-season training camp] we played well - although we managed to win 3-1 it was tricky as Leverkusen put us under a lot of pressure.
Bayern paid Hoffenheim around €13 million last month for Wagner, who was signed as back-up for their top-scoring striker Robert Lewandowski.
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.
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In Hummels' absence, Heynckes will most likely pair Niklas Suele and Jerome Boateng at centre-back.
A couple more chances fell to the visitor in quick succession in the 17th minute, with Bernd Leno forced to turn Arturo Vidal's effort from an acute angle around the post, before saving the Chilean's header from the resulting corner.
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.
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.