The Bavarians, who lead Group A with 10 points, three ahead of Manchester City, are all but assured a spot in the knockout stage with Napoli third on five points.
They can also tie up first place if they win and City fail to beat Napoli.
Villarreal, with four straight defeats, have had their worst run in form in their nine-year European history and Bayern have won a commanding 10 of their last 11 Champions League home games.
Bayern coach Jupp Heynckes will have winger Arjen Robben at his disposal after the Dutchman made his comeback against Dortmund following a six-week absence due to groin surgery.
The loss of Bastian Schweinsteiger with a shoulder injury until the end of the year, however, looks to have had a much bigger impact as Bayern were sluggish against Dortmund with their play lacking the usual pace and direction.
"We were not aggressive enough and our movement at the back was not good," Heynckes said.
Heynckes will also be without central defender Holger Badstuber who was sent off in their 3-2 win over Napoli earlier this month.
"I am certain my team will present itself differently on Tuesday," Heynckes said after the 1-0 loss to Dortmund. "One player or another seemed to be lacking the necessary tension and concentration against Dortmund. That will change."
Club CEO Karl-Heinz Rummenigge said the "painful" defeat to Dortmund should be put behind them fast.
"Now there is only victory for us on Tuesday. Then we can book our spot in the round of 16 and that is our duty," Rummenigge told reporters.
Injury-ravaged Villarreal, still without a point, have a slim chance of securing third spot and a berth in the Europa League and are not giving up yet, according to captain Gonzalo Rodriguez.
Juan Carlos Garrido's side, missing injured first-choice strikers Giuseppe Rossi and Nilmar, claimed only their third La Liga victory of the campaign on Saturday, a 1-0 home win over struggling Real Betis that put them on 14 points from 12 matches.
"You cannot be on top every year but we will always try," central defender Rodriguez told reporters. "Up to now we have known how to pick ourselves up from the reverses we have suffered, which to be honest have been a lot," he added.
"Now we have to focus on the Munich game and cling to the hope of continuing in the Europa League, although the truth is that it won't be easy and we'll have to work very hard."
Bayern Munich: 1-Manuel Neuer; 21-Philipp Lahm, 17-Jerome Boateng, 5-Daniel van Buyten, 13-Rafinha; 10-Arjen Robben, 25-Thomas Mueller, 44-Anatoliy Tymoshchuk, 39-Toni Kroos, 7-Franck Ribery; 33-Mario Gomez
Villarreal: 13-Diego Lopez; 14-Mario Gaspar, 2-Gonzalo Rodriguez, 4-Mateo Musacchio, 15-Jose Catala; 20-Borja Valero, 21-Bruno Soriano; 11-Hernan Perez, 8-Jonathan De Guzman, 3-Joan Oriol; 9-Marco Ruben
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