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Boos and whistles were aimed at Messi, Neymar and their team-mates before and during the clash at the Parc des Princes, four days after PSG was dumped out of the Champions League by Real Madrid.
Kylian Mbappe was not targeted, despite reportedly being bound for Madrid, and the in-form striker opened the scoring on with his 26th goal of the season.
Neymar then responded to abuse from his own supporters by scoring in the second half and Leandro Paredes was also on target, with Messi involved in all three goals and also hitting the post as Mauricio Pochettino's side ended a tough week with a resounding win.
PSG was almost caught cold when Remi Oudin let fly with a rasping drive that was well saved by Keylor Navas in the first minute and Jean Onana's glancing header from the resulting corner flashed just wide.
Messi and Neymar continued to be targeted by PSG fans when they touched the ball, but the Argentina captain played a big hand in Mbappe's opening goal 24 minutes in.
The former Barcelona playmaker's reverse pass found Georginio Wijnaldum, who slipped Mbappe in with a perfectly-weighted ball and the France forward finished clinically with his right foot from inside the penalty area.
Messi was then given too much time to thread a pass through to Achraf Hakimi, whose cross was coolly dinked over Bordeaux goalkeeper Gaetan Poussin and into the net seven minutes into the second half.
Although PSG was denied a penalty due to offside after a VAR check, Paredes extended his side's lead just after the hour mark with a sweet left-foot finish after showing great skill and composure to leave two Bordeaux players on the deck.
Messi struck the woodwork with a long-range strike after a surging run late on as the boos continued to sound, with Pochettino looking distinctly unimpressed with the hostility as his side cruised to victory after back-to-back defeats.
