Both sides had their chances to add to the score but it fell to debutant Cedric Bakambu to secure the points for Marseille in the 76th minute, latching on to a through ball from Guendouzi and drilling the ball home.
"I'm happy, we have the three points," Bakambu, who signed from Beijing Guoan last week, told Canal+.
"We have a good defensive base, we are good with the ball... For an attacker, it's easier to find space and to be decisive."
Marseille are now one point ahead of third-placed Nice and 10 points behind leaders Paris Saint-Germain who host Reims on Sunday. Nice will go back into second if they win at Metz.