Speaking at his pre-match press conference, the 72-year-old confirmed that top scorer Robert Lewandowski and centre-back Mats Hummels would not be fit to travel to Leverkusen for the first Bundesliga game after the winter break.
"I am happy that both have trained partly with the team and both feel well," Heynckes said of the talismanic duo.
"We will be able to increase their training schedule from next Monday, but it would be negligent to let them play. That's why both are not part of the squad."
Heynckes also added a third bit of injury news concerning Joshua Kimmich, explaining: "Joshua Kimmich will travel with the team, but I have to think about if he will start."
Kimmich has appeared in every Bayern game across all competitions this season, scoring three goals and providing ten assists.
There was one good bit of news for Bayern fans though, as Heynckes confirmed that Sandro Wagner would be fit to make his debut at the BayArena. Heynckes denied that Wagner's inclusion would change Bayern's tactics for the game though.
"I don't think it changes that much [about how they play]," Heynckes told the assembled media. "He [Wagner] is also a player who can play with his back to the opponent and make balls, like Lewy [Lewandowski].
"He has settled in well so far. He's very disciplined and impressed me in Doha. I'm happy and he'll be the first option in attack."
Wagner began his career at Bayern, making eight appearances for the first team, before embarking on a journeyman career around Germany. He rejoined the club from Hoffenheim last month.