Swede Ibrahimovic, 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.
PSG eased through with Beckham putting in a decent shift in his first start in a deep midfield position and receiving his first booking after a late clash with substitute Jordan Ayew.
The former England captain completed the most passes in the first half, including a couple of clinical crosses, three days after his 15-minute debut at the Parc des Princes.
"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.
Wealthy PSG will visit Evian Thonon Gaillard in the quarter-finals which will involve seven Ligue 1 clubs after Lorient, Girondins Bordeaux and Nancy all qualified on Wednesday.
Lorient thrashed fellow top-flight side Brest 3-0 thanks to a Jeremie Aliadiere brace and face a tough trip to St Etienne.
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.
Ligue 1 bottom club Nancy won 2-0 at fifth division Venissieux-Minguettes in extra-time to set up a clash at fellow strugglers Troyes.
In Paris, the game was nothing like Sunday's Ligue 1 battle 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.
Marseille coach Elie Baup, who expressed bitter regrets after his team had delivered a strong showing on Sunday, this time thought PSG was better.
"It's two losses on the same score (...) It's the price to pay here," he said.
"Soccer is all about the result, so we have to congratulate PSG for their performances in these two games."
The home team started well and had their first clear-cut chance through Ibrahimovic, who failed to tap in a Kevin Gameiro cross in the 15th minute.
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.
Marseille did not manage to threaten goalkeeper Nicolas Douchez until a 51st-minute Andre-Pierre Gignac long-range effort was saved.
PSG immediately reacted and pushed hard for a second goal.
Gignac blocked a Mamadou Sakho header following a neat Beckham corner in the 62nd, two minutes before right back Jeremy Morel fouled Ibrahimovic in the box.
The Swede converted the penalty to secure PSG's third victory of the season over Marseille after Sunday's league win and their Coupe de la Ligue last-16 triumph in October.
Coupe de France quarter-final draw:
(Ligue 1 unless stated)
RC Lens (II) or Epinal (III) v Bordeaux
Troyes v Nancy
St Etienne v Lorient
Evian Thonon Gaillard v Paris St Germain