The 700 passengers were victims of a power cut just after 9pm.
An SNCF spokesman told The Local that a rescue operation was hampered by the fact the incident occurred during a tunnel.
"Our normal procedures were slowed down," said the spokesman. "Also, there was no phone network available."
He added that SNCF had 100 people working on the incident overnight.
A replacement train eventually arrived to take travellers back to Marseille's main train station.
Angry passengers vented their anger as they disembarked at around 4.40am.
Several complained that train operator SNCF had not responded quickly enough.
"It was us who called the emergency services," one passenger told BFM TV. "We forced people to open the doors because people were suffering. SNCF has no idea what it's doing."
"There was no air conditioning, no beer," said another. "There were children in the train. It was really awful."
"We spent seven hours in total in that tunnel," another passenger told news channel LCI.
SNCF offered all passengers the option of spending time in a hotel if they wished although none accepted the offer.
Most passengers preferred to wait for a replacement train which SNCF provided. The train arrived at Paris' Gare de Lyon station later on Wednesday morning.
Around 20 passengers accepted SNCF's offer of a taxi back to their homes.
The company has also promised to refund all passengers double the cost of their tickets.