The visitors made the breakthrough after 22 minutes when Kevin Monnet-Paquet found the net.
Lorient raced into a 2-0 lead just moments later as Mattias Autret fired in to silence the Stade de Gerland.
Lyon began their comeback seven minutes before half time when Cris converted from Kim Kallstrom's corner.
The home side drew themselves level with 13 minutes to play thanks to Lisandro Lopez's effort.
The turnaround was secured in the 85th minute through Bafetimbi Gomis.
The win has seen Lyon go fourth in the table, while Lorient have stayed 14th.