Gignac, who had already scored in the first two matches of the season, tapped in after Valenciennes keeper Nicolas Pennetaud could only parry Andre Ayew's header from a Mathieu Valbuena corner in the 84th minute.
Last year's runners-up Marseille rode their luck in the second half after Valenciennes squandered two clear cut chances just before and after the Marseille goal.
Marseille top the table with nine points overtaking big-spending Monaco, who drew 0-0 on Friday with Toulouse.
Olympique Lyon have a chance to draw level on points with Marseille later on Saturday when they play Reims in the late game.
Champions Paris St Germain, who have drawn their first two games, travel to promoted Nantes on Sunday.