Marseille will face holders Paris Saint-Germain in the Coupe de France final following a 1-0 win at Ligue 2 side Sochaux in what was Franck Passi's first game in charge after the suspension of head coach Michel.
Passi stepped up from his role as assistant coach on Tuesday and was indebted to Florian Thauvin for settling this semi-final.
After a poor first half, Thauvin gave Marseille, who are the Coupe de France's most successful club with 10 titles, the lead shortly after the interval, the winger firing in a low finish after being found by Steven Fletcher in the box.
The victory was Marseille's second in 13 matches in all competitions and set up a showdown with PSG in the final at the Stade de France on May 21.
Werner saved an awkward bouncing shot by Georges-Kevin Nkoudou after 25 minutes, before Mandanda spilled Karl Toko Ekambi's effort, but recovered to claim the loose ball.
Fletcher found the winger in space on the right side of the box and Thauvin beat Jeando Fuchs easily and drove a superb strike inside Werner's near post.
Michy Batshuayi had a glorious chance to make sure of Marseille's win after 78 minutes, but the striker somehow put Benjamin Mendy's cross wide from eight yards out.
However, that awful miss did not matter as Marseille held on comfortably to confirm they will face PSG in May's showpiece final.
