The win secures Bayern the group’s first place with 14 points, three ahead of second-placed Lyon.
The Bavarians had Lyon’s work cut out by scoring three times in a perfect first half thanks to a Miroslav Klose double (11,37) and a Franck Ribery strike on 34 minutes.
Klose took the lead for his team on eleven minutes, after Philippe Lahm won Bayern a free kick on the edge of the Lyon box. The Germany striker stepped up and fired his effort into the top of the Lyon net.
On 34 minutes, Bayern added a second through Franck Ribery thanks to a right-footed low screamer after Luca Toni’s assist.
Jurgen Klinsmann’s men took full advantage of Lyon’s collapsing defense by scoring three minutes later. Once again it was Ribery and Klose causing all sorts of havoc in the Lyon box as the Frenchman’s cross was met by a direct Klose shot past Hugo Lloris.
After the interval, Lyon looked keen on getting back in the game, and following a saved attempt from Ederson, Sidney Govou notched one back for the hosts from close range.
Lyon added a second on 68th minute through Karim Benzema.
Despite the home side’s efforts to equalize, Bayern did well to defend their lead and win the three points.
In the group’s other game, Fiorentina ended their short-lived Champions League campaign with a 1-0 away win at Steaua Bucharest.
Italy striker Alberto Gilardino scored the only goal of the game on 66 minutes.
Cesare Prandelli’s men are now third of the group with six points, while Steaua finish fourth with a sole point from six games.