Belgian defender Daniel van Buyten gave Bayern the lead when a defensive clearance fell to him to fire home from inside the box in the 64th minute.
Midfielder Muller, who scored twice in Bayern's 5-1 Bundesliga win over Borussia Dortmund last weekend, maintained his impressive displays.
He extended the Bavarians' advantage on 85 minutes with a low shot from the edge of the area.
The 20-year-old wrapped up the victory with two minutes remaining with a close-range effort after being fed by striker Mario Gomez.
In the other Group A game, Juventus were held to a 1-1 home draw by French side Bordeaux.
The Italian side went in front three minutes past the hour mark, thanks to a goal from towering striker Vincenzo Iaquinta.
Midfielder Jaroslav Plasil secured a share of spoils on 75 minutes after a defensive lapse from Juventus.
Haifa-Bayern match goals