France forward Mbappe found the back of the net either side of the interval to take his season’s tally to seven before being replaced by Neymar as coach Christophe Galtier looked to spare the duo before PSG host Juventus on Tuesday.
The hosts were reduced to 10 men six minutes later when Fabio Da Silva was shown a straight red card for a dangerous tackle on Vitinha.
Mbappe doubled the lead nine minutes into the second half at the end of a quick counter attack. The 23-year-old found Messi in the box and the Argentine slid the ball towards Mbappe who tapped in at the near post.
Earlier, Marseille continued their near-perfect start with a solid victory at promoted Auxerre with Alexis Sanchez showing his worth with his third goal since joining from Inter Milan as a free agent during the close season.
Igor Tudor’s side prevailed through an early Gerson goal and substitute Sanchez’s late strike while Cengiz Under caught the eye with a sterling display in the first half, four days before their Champions League trip to Tottenham Hotspur in London.