Lyon, level with Ajax Amsterdam on four points, showed little ambition and tried to defend deep.
Cristiano Ronaldo glanced a corner towards the back post and Benzema slid in to score the opener against his former club in the 19th minute as Real threatened to overwhelm the visitors.
Lyon's Bafetimbi Gomis had a goal ruled out for offside in the 28th minute but it was a rare attacking foray as the chances stacked up for Ronaldo and company.
Soon after the second-half restart Benzema broke away down the left and crossed low into the centre for midfielder Khedira to stroke in the second.
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