Fofana struck from 25 yards after only eight minutes to pave the way for the visitors' success.
Bafetimbi Gomis had three clear-cut chances before he deservedly netted his 12th league goal of the season in the 28th minute as Lyon, who completely overwhelmed their harmless hosts, cruised to the victory.
Lyon are on 45 points from 22 games, three ahead of PSG who host 2011 champions Lille on Sunday. Marseille, third on 41, visit fifth-placed Rennes on Saturday.
"We were struggling with our game play since the beginning of the year. Tonight, we found it back, we dominated, we put on a very good performance," Lyon's captain Maxime Gonalons told French channel beIN Sport.
"We move forward but we know that Paris are in the race so we have to continue."
Lyon dominated possession from the kick-off and were rewarded for their good start when midfielder Fofana fired in a powerful low shot from outside the box to put them ahead.
The seven-times French champions could have doubled their lead quickly if Valenciennes' goalkeeper Nicolas Penneteau had not excelled.
Penneteau denied Gomis' first effort in the 10th minute then saved the France striker's volleyed attempt seconds later.
Gomis wasted a third chance in the 11th when he fired a Rachid Ghezzal pass well above the crossbar then he saw Penneteau carrying away another effort three minutes after.
The frontman eventually found the net when Alexandre Lacazette set him up with a neat low pass from the right following a superb collective move.
Lyon then controlled the game with keeper Remy Vercoutre playing his part when he saved Anthony Le Tallec's curling effort in the 57th.
Mid-table Valenciennes, who have won only one of their last seven league games, have 30 points.