For the first time, 10 Ligue 1 clubs went out of the competition at the first hurdle with 10 going through to the final 32.
Evian, who were still in the amateur league in 2007/08, made a brilliant start and were 2-0 up after 15 minutes.
Midfielder Cedric Barbosa opened the scoring as he latched onto an Olivier Sorlin cross in the 12th minute and striker Yannick Sagbo doubled the tally three minutes later from close range.
On a pitch churned up by torrential rain, Marseille reduced the arrears shortly before the hour when Cedric Cambon put the ball past his own 'keeper.
Evian then put the result beyond doubt four minutes before the final whistle when Kevin Berigaud headed home.
"I am very proud of my players tonight. Tonight was a great night but we now must get back to work," coach Bernard Casoni, who won the Champions League with Marseille in 1993 and managed the club in 1999/2000, told Eurosport.
Brest and AS Nancy nearly fell to amateurs, needing to go beyond the 90 minutes to advance into the last 32.
Brest were held to a goalless draw at sixth division Issy-les-Moulineaux before prevailing in extra time when Johan Martial's header gave the visitors a 1-0 win.
In front of a 3,000 home crowd gathered along the line with some lucky fans having won a seat in the tiny stands, Issy sat back and tried their luck on the counter-attack but it was not enough to unsettle the top flight club.
Nancy blew a two-goal lead at fourth division Aurillac but won a penalty shootout 4-3 after the game ended in a 2-2 stalemate.
Auxerre and Monaco fell to fifth division sides Wasquehal and Chambery respectively on Saturday.
Stade Rennes, however, showed no mercy as they thrashed third division Cannes 7-0.
