A mis-hit cross from Romain Alessandrini and a late volley from Abdel Barrada ultimately proved the difference between the two sides, but Juve also lost Sami Khedira to a hamstring injury and Stephan Lichtsteiner to a senseless red card.
Khedira, a close-season signing from Real Madrid, was carried off on a stretcher clutching his hamstring after just 25 minutes and the Germany international looks likely to miss next week's Supercoppa Italiana clash with Lazio in China.
The 28-year-old could also be a doubt for the start of the Serie A season at the end of the month, which would be a huge blow for the Turin club as they aim to retain their league title.
Moments after Khedira's premature departure, Alessandrini's ball in from the right eluded Gianluigi Buffon to give the hosts the lead and shortly before the break, Lichtsteiner managed to earn himself a straight red for dissent.
With the start of the Ligue 1 season just a week away, Marseille looked understandably sharper and fitter than the Italian champions and almost doubled their advantage early in the second half, Benjamin Mendy forcing a fine close-range save from the overworked Buffon.
Juventus, in contrast, created precious little in terms of clear-cut chances, although French star Paul Pogba did strike the frame of the goal with a stunning free kick on 68 minutes and received a standing ovation from the home fans when he was substituted moments later.
Abdel then sealed the win for the home side shortly before the end with a spectacular volley, much to the delight of the majority of the 60,000-plus crowd in the Stade Velodrome.
But if it was a grim night for Juve then it was an ideal final pre-season hit-out for Marcelo Bielsa's men, who will head into next week's Ligue 1 opener against Caen with a real spring in their step.
