Marseille, who had only beaten PSG twice since the capital side were taken over by Qatar Sport Investment (QSI) in 2011, reached the quarter-finals thanks to an Alexis Sanchez penalty and a Ruslan Malinovskyi thunderbolt after Sergio Ramos's first-half equaliser.
PSG have now lost three times already in 2023 and the Cup defeat comes less than a week before they take on Bayern Munich in their Champions League last-16 first leg.
Without the injured Kylian Mbappe, who will also miss the Bayern clash, PSG struggled and according to captain Marquinhos, they will now need to "shut (their) mouth and work" to bounce back.
"They pressed high and we did not manage to break the lines. It hurts because it was a Cup game against our great rival," Marquinhos added.
Marseille coach Igor Tudor revelled in their victory.
"Amazing guys, they're champions. It's awesome for the club," he said.
Marseille went ahead on 31 minutes when Sanchez converted a penalty after Cengiz Under had been brought down by Ramos, giving the hosts a deserved advantage after a lively start.
Ramos, however, made up for his mistake as he headed home Neymar's corner two minutes into first-half stoppage time, shortly after the Brazilian had hit the post with an 18-metre strike.
The Velodrome stadium then came to the boil when Malinovskyi, who joined on loan from Atalanta last month, beat Gianluigi Donnarumma with a vicious half-volley from just outside the box that went into the top corner.
Ramos had a goal disallowed for offside in added time in a nail-biting finale as Marseille defended tooth and nail.
