Visitors Marseille, fielding a largely second-string team, went ahead in the 19th minute thanks to Michy Batshuayi's strike but Rennes levelled on the hour through Anders Konradsen.
The Brittany side wrapped it up three minutes into stoppage time when Philipp Hosiner netted with a back heel.
It was the Ligue 1 leaders' second defeat in a row after they suffered a 1-0 loss at Olympique Lyonnais in the league last weekend.
(Reporting by Julien Pretot; Editing by Toby Davis)
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