United's second oldest ever line up in the Champions League ensured the Premier League leaders and FA Cup semi-finalists joined Europe’s elite in the last eight.
Yet it required two goals from 22-year-old Javier Hernandez to calm nerves on the most tense of Old Trafford nights.
United had already established a two-goal cushion when Wes Brown’s own goal set up a grandstand finish.
But make no mistake, this was a close shave and Marseille headed back to the south of France knowing they had missed a glorious opportunity to eliminate Ferguson's team in their own back yard.
United’s night had started badly with the news Nemanja Vidic would not feature because of a damaged calf.
It improved, thanks to Hernandez, before finishing with the news that John O’Shea and Rafael are both expected to be out for three weeks because of hamstring injuries.
“When you look at the games we have had over the past few weeks — it is a big demand on the players and that catches players out,” said Ferguson, who is without 12 players due to injury and suspension.
“We will have to see [if Vidic is back for the weekend]. Johnny Evans has started training and we are hopeful about having him for Saturday.”
United did little to counter Didier Deschamps’ claim that they lacked “fantasy” during a turgid stalemate on the Cote d’Azur three weeks earlier, a comment which clearly irritated Ferguson.
“I hope that we can show Didier Deschamps that despite his suggestion that our present side doesn't have as much fantasy compared with our team of a few years ago, we are still capable of producing our fair share of magic,” wrote the United manager.
“I take his point because the side that captured the unique treble was something quite special,” he added before warning, “but don’t underestimate the boys of today.”
Marseille certainly could not be accused of taking United lightly but from the opening minute they found the Premier League leaders a much more adventurous unit on home turf as the visitors were forced to guard against conceding an away goal.
The French defence held out for all of five minutes before Hernandez broke the deadlock.
Started by the excellent Wayne Rooney, the move which unlocked the visitors’ defence ended with the England striker squaring for his forward partner to side-foot into the net from five-yards.
Suddenly, the Marseille supporters who braved Old Trafford in mid-March without a shirt on their backs were feeling the cold, yet they could so easily have been celebrating an equaliser before half-time.
Andre Ayew’s flick sent in-form striker Andre-Pierre Gignac clean through with only Edwin van der Sar to beat, but his first-time finish was dreadful and United breathed a sigh of relief.
That, and Souleymane Diawara’s header which whistled narrowly wide, served as a reminder that, despite the lead, the hosts still needed to score again to put the result beyond doubt.
United ended a hectic half by having a penalty shout turned down after the busy Hernandez appeared to have been clipped by Taye Taiwo before Rafael’s night was curtailed by injury.
Fortunately, United did not buckle from the double injury set back, Hernandez finally getting his second 15 minutes from time after firing home Ryan Giggs’s low cross from seven-yards following good work by Antonio Valencia.
Still United could not relax as Brown’s late own goal set up a grandstand finish before United were able to celebrate making it into Friday’s draw.
“We were nervy because we kept on getting players taken off with injuries and that affected the balance of the team,” added Ferguson.
“I thought we looked quite comfortable and then O’Shea is off, Da Silva is off. I could have brought on Darron Gibson to add a bit of height.
“The problem for us was going to be height because their set pieces are very good and they caused us a few problems.”
Rooney said of two-goal Hernandez: “He’s got great movement so I’m playing the position that I did when I started playing professionally. I’m enjoying it and thankfully he’s a finisher.”
Manchester United subs: Rafael for O’Shea, 36, Fabio for Rafael, 69; Valencia for Nani 61.
Marseille subs: J Ayew for Mbia 80, Valbuena for 69.