Killed were Amtrak's engineer Michael Kempf, 54, of Savannah, Georgia, and conductor Michael Cella, 36, of Orange Park, Florida, Lexington County Coroner Margaret Fisher said on Sunday.
The southbound passenger train's locomotive was lying on its side, and the first vehicle was bent and also derailed, although it remained upright, according to images from the scene in the small city of Cayce, South Carolina.
Investigators say a switch was turned, forcing the train onto a side track where the freight train was parked.
The Silver Star, en route from NY to Miami with almost 150 people aboard, was going an estimated 59mph when it struck the empty CSX train at around 2.45am, Governor Henry McMaster said. That train had two locomotives and 34 empty auto racks used to transport cars, the NTSB said.
Lexington County Sheriff's spokesman Adam Myrick says deputies were taking the uninjured in patrol cars to a shelter.
Anderson said dispatchers at CSX were manually routing trains around 2:45 a.m. Sunday. She said family members were "very distraught" and "very shocked".
Sumwalt said, ironically, that indications were that the system created to help stop trains before a collision was being prepared to be installed on the track.
Anderson was referring to a crash on Wednesday, Jan. 31, when an Amtrak train carrying some Republican members of Congress and their families smashed into a garbage truck on the tracks in Crozet, Virginia.
PTC has received a lot of attention in the USA as it has taken a long time to implement and could have been a safeguard against many accidents that have happened.
Throughout the several next days, NTSB investigators will "thoroughly document" the accident site, Sumwalt said.
Sunday's was just the latest fatal incident involving an Amtrak train in the past few weeks.
Speaking in a phone conference call with reporters, Anderson says the crash of the train heading from NY to Miami shows why the USA needs to install positive train control by year's end.
In a statement, Amtrak said that it was "deeply saddened" by the deaths and added that it was cooperating fully with the NTSB, as did CSX.
Officials said that about 115 other Amtrak passengers had been transferred to local hospitals.
A train collision in SC has left at least two people dead and at least 116 injured.
The system is in place in the Northeast, but Anderson says private companies who run the tracks Amtrak uses elsewhere have in the past asked for extensions to deadlines.
In an announcement on Twitter, the US Government's National Transportation Safety Board (NTSB) said: "NTSB has deployed a go-team consisting of experts in rail operations, mechanical, survival factors, human performance, recorders and signalling".
President Donald Trump tweeted his condolences around midday.
I would like to particularly thank the Cayce Department of Public Safety as they were first to arrive on this horrific scene as well as the surrounding police, fire and EMS crews that were all quick to respond. "Nobody was panicking", said Pettaway, who was discharged from a hospital with minor whiplash.
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