The German side secured their win thanks to a second half strike by Martina Mueller.
The win ends a run of 118 games without defeat in all competitions for Lyon, who won the competition in 2012 and 2011.
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Since Guus Hiddink arrived at the helm, Chelsea have improved considerably after a tricky start to the campaign.
Newcastle United are staring down the barrel of relegation to the Championship for the second time in the past eight years.