Both Bayern and Valencia have 10 points and will progress from the group to the last 16 regardless of Wednesday's results.
The Bundesliga side know a win will be enough to earn them the sought after first place and will be confident against BATE Borisov, who have struggled in the group after they won their first two games which included a shock 3-1 defeat of Bayern.
Bayern boss Heynckes was in a defiant mood when speaking to reporters ahead of Wednesday's clash.
"We have to get stuck in properly, this is not a friendly game," Heynckes said.
A first-placed finish could earn an easier path through the last 16, but the 67-year-old knows this competition takes no prisoners when it reaches the knockout stages.
Real Madrid and AC Milan look set to fill runners up spots in their respective groups and Heynckes is not expecting an easy passage.
His plans were also dealt a blow after centre back Holger Badstuber underwent surgery on Monday for cruciate ligament damage suffered in his right knee during last weekend's 1-1 draw against champions Borussia Dortmund.
Heynckes said: "Either way, it is difficult in the second round.
"Holger's loss is a big loss. I hope that we can compensate for that in other areas."
Jerome Boateng and Dante are likely to fill-in the the centre of defence but Luiz Gustavo and Arjen Robben will also miss out for Bayern due to injury.
Midfielder Bastian Schweinsteiger knows his side need to avoid complacency following Bayern's defeat by BATE earlier in the tournament.
"It was a warning to us all," Schweinsteiger told Bundesliga.de. "BATE aren't a team that you can just turn up against and win 5-0.
"They almost got a draw in Valencia and they shouldn't be underestimated."
BATE coach Viktor Goncharenko approaches the game knowing his side have booked their place in the Europa League due to a better head-to-head record against Ligue 1 side Lille.
There are no fresh injury worries for the Belarusian side, and Goncharenko could name the same starting XI that defeated Shakhtyor in the domestic league last weekend.
BATE midfielder Edgar Olekhnovich knows Bayern might be seeking to avenge their 3-1 defeat in Minsk but he is not focussing on that aspect of the match.
"It was a truly memorable game, it will not be forgotten," Olekhnovich told BATE's official website. "Moreover, we did not win by accident.
"For God's sake, let Bayern grind their teeth. I'm excited about the game and I'm not paying attention to that.
"No one is speaking about our rival's desire for revenge in this team."