It was the visitors who took the lead through a fine header from Gil to make it 1-0 after 12 minutes.
Lyon went searching for an equaliser and found one on 18 minutes through Michel Bastos.
Lyon continued to dominate and won a penalty on 21 minutes. Bafetimbi Gomis stepped up to take the spot-kick and kept his cool to give the home side a 2-1 lead.
Alexandre Lacazette had an effort on goal on 26 minutes but failed to hit the target.
Valenciennes began to push for an equaliser themselves and could have drawn level but for Gael Danic's poor finish on 29 minutes.
The half-time whistle blew with Lyon leading Valencienne 2-1.
The away side chased for an equaliser after the restart but failed to hit the target with their efforts.
They soon paid for their missed chances when Clement Grenier gave Lyon a 3-1 lead on 69 minutes.
After 76 minutes, Gregory Pujol pulled a goal back for the visitors, who were now hunting for a late equaliser.
However, Valenciennes could not break through and Lyon held on to claim the win.