Lyon, playing in Europe's premier club competition for the 11th time in a row, were stronger than the Germans and took the lead after 21 minutes through Brazilian Michel Bastos but they failed to score again despite having the numerical advantage.
"I think we could have done a better job in the second half and scored that second goal," Lyon coach Claude Puel told French TV channel TF1. "We did some interesting things, we made them run and we were the best side physically."
However, Lyon never totally outplayed Schalke 04, although the visitors were themselves barely a threat following Jefferson Farfan's missed chance in the 11th minute.
Lyon's big-money close season signing Yoann Gourcuff, who inspired Girondins Bordeaux to scintillating performances in the group phase last season, had little impact in midfield.
Even if he had done a better job, Gourcuff would have found it hard to find Argentine striker Lisandro Lopez, who seemed out of sorts and was barely in the match at the Gerland stadium.
Lyon were lucky to find themselves playing against 10 men following Benedikt Hoewedes's harsh red card in the 38th minute for a rough, although not dangerous, tackle on Jimmy Briand.
France striker Briand left the field but quickly returned although he did little to inspire Lyon, who were lucky to have Bastos and talismanic keeper Hugo Lloris in their team.
The Brazil winger cannily intercepted Christoph Moritz's header and lifted the ball past Manuel Neuer for the only goal.
The goal inspired Bastos who became the most dangerous Lyon player on the pitch, providing a string of fine crosses that the French side's misfiring strikers failed to make the most of.
France keeper Lloris just had a couple of saves to make to deny Farfan and Moritz before the interval, stretching to his right as the ball looked set to hit the back of the net.
"It's good for our confidence. It's good to get such a result before the Bordeaux game," said Puel whose side visit the Girondins in Ligue 1 on Sunday having picked only five points from their opening five domestic league games.
