The 1-0 loss to Dortmund was a blow in Bayern's bid to reclaim the domestic crown they relinquished to Jurgen Klopp's men in May but they remain two points clear at the summit.
They have found life equally straightforward in Europe, with three wins from their four Group A matches taking them clear of big-spending Manchester City.
A draw against Villarreal would guarantee them a place in the knockout phase, while a win would secure them top spot should City fail to win at Napoli.
Coach Jupp Heynckes said: "We have big ambitions in the Champions League.
"It is good that on Tuesday we already have the next game.
"I think we have digested the defeat against Dortmund and I am confident that we can defend our leading position in the group."
Heynckes has come in for criticism for starting Arjen Robben against Dortmund despite the winger lacking match practice but the former Bayer Leverkusen boss says the Holland international will play against Villarreal.
"Arjen needs match practice. Of course he will play from the start," he said.
Villarreal have lost all four matches in the pool and need to win and against Napoli on matchday six to stand any chance of clinching third place and a spot in the Europa League.
Juan Carlos Garrido's side have struggled domestically and in continental competition this season.
But three successive clean sheets in the Primera Division suggest they may have found something to build on.
Defender Gonzalo Rodriguez said: "The situation is not easy, but the team has come together and we are trying to find our way.
"Three games with a clean sheet was a key step and we have managed to do it.
A Borja Valero goal was enough to give Villarreal a 1-0 win over Real Betis at the weekend, a result which lifted the Yellow Submarine up to 12th in the standings.