Messi's expected departure from the French giants after two seasons was officially confirmed by PSG in a statement shortly before Saturday's game.
"His contribution to Paris Saint-Germain and Ligue 1 cannot be underestimated and we wish Leo and his family all the best for the future," said PSG president Nasser al-Khelaifi.
Yet Messi's name was jeered by some fans as the teams were announced at the Parc des Princes and the Argentinian World Cup winner was again whistled sporadically during the match.
There was little riding on the game itself after PSG wrapped up a record 11th French title last weekend, and Christophe Galtier's side contrived to throw away a two-goal lead.
Sergio Ramos, whose own departure from PSG was confirmed on Friday, marked his final appearance by heading in a Vitinha cross for the opener in the 16th minute.
Tribute to injured Rico
Mbappe, looking to end a fifth consecutive season as Ligue 1's top scorer, then scored a penalty to make it 2-0 with his 29th league goal this season, which he marked by holding up goalkeeper Sergio Rico's number 16 jersey.
Spaniard Rico, PSG's back-up goalkeeper, is in a serious condition in hospital in Seville after being injured in a horse-riding accident last weekend.
"The most important thing was the tribute to Sergio," Mbappe told broadcaster Canal Plus.
"There are more important things than football, and on the pitch we were already champions. We could have lost 22-0 and that would not have changed anything for us.
"We had to pay tribute to Sergio. I think we have all been affected by what is an extremely serious situation. We have been worried about that all week and so we tried to pay tribute in the best possible way.”
Mbappe's goals tally left him two ahead of Lyon's Alexandre Lacazette in the final standings.
Johan Gastien pounced on a Marco Verratti mistake to pull a goal back for Clermont, who then saw Grejohn Kyei miss a penalty.
The visitors then equalised in first-half stoppage time when Mehdi Zeffane netted from close range after Gianluigi Donnarumma spilled the ball.
Kyei got Clermont's winner in the second half when he turned in a cross with his knee.
A famous win for Clermont sees them finish the season in eighth place.
PSG picked up the championship trophy after the game but end the season with seven league defeats, all of them suffered in 2023.
