Winger Hatem Ben Arfa created the goal in the 85th minute with a driving run before laying off for Kallstrom to fire under Jussi Jaaskelainen at the near post.
New signings Gavin McCann and Jlloyd Samuel started for Sammy Lee's side but Lyon dominated the opening period.
Abdulkader Keita headed against the crossbar early on before Nicolas Anelka tapped home for the Trotters, only to be ruled offside.
Bolton improved after the break by Lyon still created the bulk of the chances, and Jaaskelainen had to be at his best to keep out Milan Baros before Kallstrom struck.
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