The Swede, who had sealed PSG's 2-0 home league victory in added time on Sunday, opened the scoring in the 30th minute and made it two from the penalty spot in the 63rd.
Ibrahimovic has scored five goals in three matches played against Marseille this season, having already found the net twice in the league game at the southern side.
"He made a very good performance. He made good passes as usual, he was well positioned on the pitch alongside Blaise Matuidi. He was very solid," PSG coach Carlo Ancelotti said.
Girondins Bordeaux eliminated fourth-tier Raon L'Etape on penalties after labouring to a 2-2 draw and will play at Ligue 2 side Lens or third division Epinal, who play on Thursday.
In Paris, the game was nothing like Sunday's Ligue 1 match in which Marseille dominated possession and had the best chances.
"We played much better than we did on Sunday. It was a different game. Marseille were more defensive thus it was easier for us to have the ball. We were stronger, more aggressive and we controlled the game," Ancelotti said.
"It's two losses on the same score... it's the price to pay here," he said.
"Football is all about the result, so we have to congratulate PSG for their performances in these two games."
Jeremy Menez, who was wearing the captain's armband for his first start in four games, struck high above the crossbar two minutes later.
With Beckham doing a good job in building and directing the play, PSG continued to pile the pressure on Steve Mandanda's goal and Ibrahimovic saw his powerful attempt parried away by the goalkeeper only a minute before breaking the deadlock.
The Swede ran onto a superb Clement Chantome pass and resisted Lucas Mendes' challenge to slip the ball between Mandanda's legs.
