Bayern paid Hoffenheim around 13 million euros ($15.4m) last month for Wagner, who was signed as back-up for their top-scoring striker Robert Lewandowski.
The Poland star is returning to full training after a knee injury, but Heynckes opted to start Thomas Mueller up front for Bayern at Leverkusen with Wagner on the bench.
While goalkeeper Manuel Neuer is still recovering from a fractured foot, Mueller also wears the captain’s armband for Bayern.
With Mats Hummels out with a groin injury, Niklas Suele partners Jerome Boateng at centre-back.
Leverkusen coach Heiko Herrlich started Jamaica’s Leon Bailey on the left wing with Germany pair Julian Brandt and Kevin Volland forming a potent force up front.
The Bundesliga resumes on Friday with Bayern 11 points clear in the table at fourth-placed Leverkusen, who are on a 12-match unbeaten run.
The Bavarian giants have not won at Leverkusen’s BayArena since 2013.
Bayer Leverkusen (4-1-3-2)
Bernd Leno – Wendell, Sven Bender, Jonathan Tah, Lars Bender – Dominik Kohr – Leon Bailey, Kai Havertz, Karim Bellarabi – Kevin Volland, Julian Brandt
Coach: Heiko Herrlich (GER)
Bayern Munich
Sven Ulreich – David Alaba, Jerome Boateng, Niklas Suele, Rafinha – Javi Martinez – Franck Ribery, James Rodriguez, Arturo Vidal, Arjen Robben – Thomas Mueller
Coach: Jupp Heynckes (GER)
Referee: Daniel Siebert
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