Officials say it happened approximately 5:16 p.m. Monday as the six-car train headed eastbound towards the bridge.
"We got a report of smoke on the tracks and the train was in the tunnel and the train was shut down," said Battalion Chief Robert Clark.
Firefighters and police converged on the scene. However authorities say the train did not fill with smoke and there was never evidence of an actual fire.
Nearly 750 passengers were onboard and they smelled the smoke and felt the train come to a stop just as it started out of the tunnel.
"The conductor said not to panic that she was shutting the engine off and that we were most likely going to have to evacuate towards the back of the train," said Megan Kowalski.
"I was panicking a little in the beginning just because the smoke was so horrible and I just didn't know what was going on," said Michelle Butvilas.
Butvilas snapped some cell phone photos as firefighters boarded the dark train. For a long time everyone just waited.
"Everybody was very calm. Nobody was getting upset. Everybody started texting families and letting them know what was going on," said Melinda Lamb.
Then, they were escorted car by car out of the back of the train to an abandoned PATCO station beneath Franklin Square where another train was waiting to take them on their way.
"Once we got off the train, it was pretty dark but there were firefighters all along the route," said Butvilas.
Some didn't want to board another train and climbed the stairs into the open air where they had other rides waiting.
The last person escorted out was the train's operator - who was given oxygen and taken away in a waiting ambulance.
PATCO officials found that the smoke came from a short in the motor.
Two passengers were checked out at the scene but not transported to the hospital.