Mbappe gave PSG a taste of what they would be missing if he left for Real Madrid, who have made bids to recruit the France striker since Messi joined on a two-year deal from Barcelona.
PSG are top of the standings with a maximum 12 points.
All 20,545 tickets available were sold at the Auguste Delaune stadium to see 34-year-old Messi play and the fans, who chanted the Argentina forward's name, were rewarded in the 66th minute when he replaced the disappointing Neymar.