Bayern, a four-time European champion, had a comfortable evening in Switzerland after Mario Gomez finished a simple breakaway move in the seventh minute.
In other playoffs, Giuseppe Rossi’s two second-half goals helped lift Villarreal to a 3-1 aggregate win over Odense, and Dinamo Zagreb and APOEL also advanced to the group stage.
Five more playoffs are concluded Wednesday to complete the 32-team Champions League lineup. UEFA conducts the draw in Monaco on Thursday.
Bayern has an extra incentive to succeed this season as its home stadium hosts the final next May.
Bayern’s plans were disrupted when coach Jupp Heynckes left Arjen Robben on the bench, after the Netherlands winger felt a recurrence of back pains.
Zurich is off to a slow start in the Swiss league but threatened in the fifth minute when Amine Chermiti fired a left-foot shot just wide from 20 meters (yards).
Two minutes later, the Swiss defense was exposed by a simple ball to Bayern forward Thomas Mueller on the right touchline. Mueller sent Gomez clear in the middle and the big forward slotted the ball low inside goalkeeper Johnny Leoni’s right hand post.
Bayern goalkeeper Manual Neuer was unconvincing dealing with crosses, and used an unorthodox low punch to clear Ricardo Rodriguez’s 24th-minute free kick.
Gomez had a clear chance from a stoppage-time corner but the ball struck his shoulder and flew over.
Zurich missed a chance to put pressure on Bayern in the 55th when Swiss international forward Admir Mehmedi shot wide from inside the penalty box.
Nils Petersen, who replaced Gomez at half time, went close in the 59th and then was denied by Leoni’s diving save in the 76th.
Villarreal’s 3-0 win over Odense overturned a 1-0 first-leg deficit, but only after failing to convert early dominance into goals.
Rossi leveled the tie in the 50th minute, forcing home Nilmar’s cross from the right, and 16 minutes later the Italy forward connected on Cani’s cross with a left-foot volley.
Both teams were then reduced to 10 men. Odense’s Bashkim Kadrii collected a second yellow card, and Villarreal’s Borja Valero got a straight red for butting Andrea Johansson in the chest.
Substitute Carlos Marchena 82nd-minute shot crept into the net due to a mistake by the otherwise excellent Odense goalkeeper Stefan Wessels.
APOEL of Cyprus needed an 87th-minute goal from Brazilian forward Ailton, his second, to secure a 3-1 win on the night, 3-2 on aggregate, against Poland’s Wisla Krakow.
Croatian champion Zagreb advanced 4-3 on aggregate despite a bold comeback by Sweden’s Malmo, who were 2-0 winners Tuesday with goals from Wilton Figueiredo in the 69th and Pontus Jansson in the 86th.
In Wednesday’s playoffs, Arsenal takes a 1-0 lead to Udinese, Lyon has a 3-1 advantage in Russia against Rubin Kazan and Czech champion Viktoria Plzen defends a 3-1 lead at home to Copenhagen.
Benfica hosts FC Twente after a 2-2 draw in the Netherlands and Sturm Graz resumes in Austria at 1-1 against BATE Borisov of Belarus.