The France striker came off the bench to score the opening goal as Thomas Tuchel's side made it 11 wins from 11 at the start of the season.
Kylian Mbappe described himself as a leader after helping Paris Saint-Germain to a win over Marseille despite starting the match on the bench.
The 19-year-old broke the deadlock three minutes after coming on in the second half at Stade Velodrome, before playing a part in Julian Draxler's injury-time strike that secured a 2-0 win.
Mbappe was surprisingly left out of the starting line-up, which coach Thomas Tuchel later confirmed was a punishment following a breach of discipline , with the forward arriving late for the pre-game team talk along with Adrien Rabiot.