The last seven coaches of the train came off the track as the front of the train entered the Saint-Charles station at just before 6.00pm.
The train, which had left Paris at 2.37pm, was travelling at just 27km/h and none of the 350 passengers was injured, the SNCF said.
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But 15,000 passengers' journeys were affected on Friday evening and regional SNCF boss Jean-Aimé Mougenot predicted disruption to traffic for several days because of repair work to the rails.
Removing the train was expected to take until at least Sunday, he told a press conference on Saturday morning.
Only nine of the station's 16 platforms were in operation on Saturday and, while TGV and Ouigo trains would be running, regional services to Aubagne, Aix-en-Provence and Miramas were expected to be seriously affected.
In November 2015 11 people died when a Paris-Strasbourg TGV came off the rails, the only mortal accident involving the high-speed trains to have taken place.
The last derailment in France was of a Paris regional train in June.
Seven people suffered slight injuries in that accident.