Bayern took control of their play-off tie against FC Zurich with a 2-0 first-leg win at their Allianz Arena home, which will host the competition final on May 19.
Bastian Schweinsteiger gave the hosts an eighth-minute lead when he headed home a left-wing cross from Arjen Robben, who doubled Bayern's lead 18 minutes from time with a glorious curling effort into the top-left corner.
Jupp Heynckes' side, seeking a reversal in fortunes after a forgettable 2010-11 campaign that saw them finish third in the Bundesliga, would have won even more handsomely but for several near-misses in the second half.
Mario Gomez, Philipp Lahm and Franck Ribery - who hit the post - all spurned chances prior to Robben's goal, while Gomez also sent a late chance over the crossbar.
The visitors, who finished second in the Swiss top flight last season, finished the game with 10 men after defender Mathieu Beda was shown a second yellow card in injury time.
"The players knew how important this game was for us," said coach Heynckes, who joined from Bayer Leverkusen at the end of last season.
"We started well in the first 20 minutes and created some good chances, but if you are as superior in the second half as we were, we have to take our chances. We have to raise our tempo against a team like that."
Bayern will be strong favourites to progress ahead of next Tuesday's second leg, but Villarreal's hopes are in the balance after a 1-0 loss at Danish underdogs Odense, who have never previously reached the group phase.
The Spanish side, beaten by eventual champions Porto in last season's Europa League semi-finals, created the clearer chances but were undone by a nightmare moment for debutant Cristian Zapata.
The Colombian centre-back, a summer signing from Udinese, handed the winning goal on a plate to the hosts with a weak back-pass that allowed Odense forward Hans Henrik Andreasen to pounce in the 84th minute.
Villarreal had looked the more threatening side up to that point, with strike duo Nilmar and Giuseppe Rossi thwarted by home goalkeeper Stefan Wessels on several occasions.
Elsewhere, Croatian champions Dinamo Zagreb all but booked their group stage ticket with a 4-1 win at home to Malmo, who eliminated Scottish giants Rangers in the previous round.
Maccabi Haifa won 2-1 at home to Genk, while Polish champions Wisla Krakow prevailed 1-0 against Cypriots APOEL Nicosia in the home leg of their tie.
In Tuesday's matches, a Theo Walcott goal gave Arsenal a slender 1-0 win at home to Udinese, while 2010 semi-finalists Lyon beat Rubin Kazan 3-1 at Stade Gerland and two-time champions Benfica secured a 2-2 draw at FC Twente.
The second legs take place on Tuesday and Wednesday next week.
Bayern win, Villarreal in Champions League peril
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