Desire Doue and Ousmane Dembele found the back of the net while Willian Pacho and substitute Lucas Hernandez were sent off for the European champions at the Mercedes-Benz Stadium in Atlanta, Georgia.
The game remained scoreless until PSG winger Doue found the breakthrough in the 78th minute, wrongfooting Manuel Neuer at the near post.
The French club were then reduced to nine men, as defensive duo Pacho and Hernandez each received straight red cards within the space of 10 minutes.
Despite a numerical disadvantage, Dembele wrapped the game up with PSG's second goal in stoppage time, though Bayern had a penalty disallowed by VAR in the final minutes of the match.
There was a horror injury to Bayern Munich attacker Jamal Musiala after his leg got stuck underneath goalkeeper Gianluigi Donnarumma's body.
The 22-year-old Musiala's left ankle seemed to be fully twisted, indicating a possible broken leg/ankle and maybe more.
PSG will face either Spanish club Real Madrid or German outfit Borussia Dortmund in Wednesday's semi-final.
The stage is set for a blockbuster quarter-final in the FIFA Club World Cup as Bayern Munich face off against Paris Saint-Germain in a match that promises high stakes and fierce competition on Saturday.
Real Madrid are set to lock horns with Borussia Dortmund in the FIFA Club World Cup quarter-finals on Saturday evening at MetLife Stadium in East Rutherford, New Jersey.
At the FIFA Club World Cup in Philadelphia, Chelsea and Fluminense emerged victorious in their quarter-final clashes, securing semi-final berths with hard-fought 2-1 wins over Palmeiras and Al-Hilal, respectively.
Bayern Munich are gearing up for an electrifying quarter-final clash against Paris Saint-Germain in the FIFA Club World Cup on Saturday, with Thomas Muller anticipating a fiercely competitive battle.
