Thierry Henry scored the second half winner on his return to France but the goal was made in England by young defender Ashley Cole.
Left back Cole produced a mazy run into the penalty area in the 59th minute and beat defender Eric Deflandre to find Henry who made no mistake with his jump and finish.
Lyon dominated the match but their attacks broke apart on the Arsenal defence but the English club owe their win to veteran goalkeeper David Seaman.
Lyon's luck was out from early in the game when Ashley Cole handballed in the 11th minute but no penalty kick was awarded.
Seaman's best save of the night saw him defy Steve Marlet when he was put clear adn bore down on the goal. Henry came close when he hit the outside of the post on a counter attack in the 42nd minute.
The win was Arsenal's first in the second phase but other results are going well for the London club who fielded four Frenchmen on their trip to Lyon and they are well placed in contention to qualify behind Bayern Munich.
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