Lyon enjoyed more of the possession in the early stages but they struggled to create many clear chances and almost fell behind when Chris Malonga struck an effort just wide of the post midway through the first half.
Abdoulaye Ba came even closer when he headed just over the crossbar after being allowed too much space inside the box.
However, the visitors continued to look dangerous and they took the lead in the 39th minute when Moussa Maazou controlled a long pass before firing the ball into the bottom corner.
Lyon were frustrated in the closing stages when Alexandre Lacazette looked to have won a penalty following a challenge from Ba but the referee changed his mind just moments later and gave the hosts a corner.
The home side were dealt another blow in stoppage time when Maazou was shown a second yellow card for persistent fouling.