Radamel Falcao scored a hat-trick to continue the defending champions’ perfect start to the season.
Mbappe was named as a substitute by boss Leonardo Jardim, nine days after he limped off in their 3-2 win over Toulouse, amid speculations linking him with a move to Paris Saint-Germain.
Jardim failed to summon the 18-year-old, as Falcao took centre stage at the Stade Gaston Gerard.
“It’s a club decision not to have him start the game,” Jardim said after the match.
“In the end, the game went smoothly and I gave the opportunity to other players to help make the building of the team more effective.
“In the coming months, with the Champions League, we’ll need everyone. We have to give rhythm to those who aren’t often used.”