Memphis Depay, who has been linked with a move to Barcelona, and Moussa Dembele were both in the Lyon starting line-up but neither figured strongly in a lacklustre performance.
"It was an awkward game," midfielder Bruno Guimaraes said.
"We missed chances, some easy ones in particular. We need to work more because we can't lose points like that."
The home side has not won since the opening round of games and looked a shadow of the side that reached the semi-finals of the UEFA Champions League and lost to Paris Saint-Germain in the French League Cup final in August.
After four games, Lyon is down in 10th place on the table with just one point more than Nimes.
Earlier in the day, Lyon announced the signing of German goalkeeper Julian Pollersbeck from Hamburg for €250,000 euros ($404,950) as deputy to Anthony Lopes.