Reiten curled a first-time effort low beyond goalkeeper Christiane Endler just before the half-hour for the visitors, a fine finish coming after an outstanding piece of play by Scotland's Erin Cuthbert to create the chance.
The result puts Emma Hayes's Chelsea - runners-up two years ago - in the driving seat as they seek to become the first English winners of the competition since Arsenal in 2007.
Chelsea had already beaten France's other heavyweight, Paris Saint-Germain, home and away in the group stage, yet Lyon's pedigree in Europe is second to none.
They won the title last year for the sixth time in the last seven seasons, and Sonia Bompastor's team will still hope to turn this tie around in next week's return.
The visitors could have been further in front before the interval, with a Lauren James shot coming back off the post.
Yet Lyon had chances too, despite former Ballon d'Or winner Ada Hegerberg starting on the bench as she recovers from her latest long injury lay-off.
Delphine Cascarino hit the woodwork in the second half for Lyon, who have won the Champions League a record eight times overall.
