The Parisians, inspired by captain Pedro Pauleta, who scored a goal and set up another, beat Nantes 2-1 away.
The final on April 29 will be Marseille's first for 15 years since losing to Monaco in 1991, while it will be the sixth for PSG since 1993.
"We wanted to go to the Stade de France because we have been waiting for this for a long time," Marseille coach Jean Fernandez said."
The last meeting between the two clubs -- in March -- resulted in a French Football Federation (FFF) ethics commission hearing because Marseille fielded a B team and asked their supporters not to travel to the match in Paris citing security fears.
"It's going to be a dream final against Marseille," said Paris midfielder Edouard Cisse. "It's going to be the match everybody wants to see."
Marseille produced their best performance of the season to settle the tie at their Stade Velodrome in the first 45 minutes.
Midfielder Franck Ribery, tipped by many to earn a place in France's World Cup squad, grabbed the first goal after just 17 seconds, scoring with a composed lob after a blunder from central defender Gregory Bourillon.
Nigerian defender Taye Taiwo blasted home a free-kick for the second goal on 18 minutes and Mamadou Niang added a third on the stroke of halftime.
"I'm really happy with my performance today," said Ribery, given a standing ovation after his substitution 10 minutes from time.
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An injury doubt for PSG before the match, Ligue 1's leading scorer Pauleta recovered in time to start at Nantes.
The Portuguese set up striker Fabrice Pancrate in the 68th before sealing the game with a crossed shot four minutes from time after Nantes pulled one back through defender Mauro Cetto.
"He (Pauleta) said he felt better when we arrived here," PSG coach Guy Lacombe said. "So I decided to give him a try and he was great."
"I'm really proud of what we did tonight. We fully deserved to win," he added.