- Sergio Ramos (16')
- Kylian Mbappé (21' Pen)
- Johan Gastien (24')
- Mehdi Zeffane (45'+1')
- Grejohn Kyei (63')
PSG confirmed before kick-off that Messi would not extend his two-season stay at the club beyond this campaign, making this his farewell to supporters.
Some of the PSG faithful booed Messi when the Parc des Princes announcer read his name before Saturday's match began. A few minutes later, Messi walked onto the field with a smile on his face, holding his three children's hands before the team photo and kissing them on their foreheads.
"I would like to thank the club, the city of Paris and its people for these two years. I wish you all the best for the future," Messi told the club website.
In two seasons at PSG, Messi won two French league titles and the French Champions Trophy while notching 32 goals and 35 assists in all competitions.
The Paris club sealed the Ligue 1 title last weekend, but the campaign has been a disappointment following a round-of-16 exit in the Champions League for a second successive season, and the club's fans have made their displeasure known in recent weeks.
Sergio Ramos opened the scoring in what was also his final game for PSG when he headed in a deep cross from Vitinha, before Kylian Mbappe made it 2-0 from the penalty spot for his 29th goal of the season that helped him secure the Golden Boot.
Clermont did have their equaliser on the stroke of half-time, though, when the ball rebounded kindly to Mehdi Zeffane, and he tapped home.
Messi had a golden chance to put PSG back in front after being set up by Mbappe, but the World Cup winner skied his shot high over the bar when one-on-one with the goalkeeper. The miss was followed by audible boos and whistles from the club's supporters.
Kyei then finally got his goal with a close-range finish just past the hour mark to give Clermont the win.
The PSG players and technical team received the Ligue 1 trophy after the game, but there were also loud boos from around the stadium for coach Christophe Galtier, who took charge of his 50th, and possibly last, fixture with the side.
It was an emotional night in Paris, where players from both sides paid tribute to PSG goalkeeper Sergio Rico, who remains in intensive care following a horse riding accident in Spain last weekend.
Information from Reuters and The Associated Press was used in this report.
- Thomas Leonard