The two train drivers, both men from Port Augusta aged 48 and 57, died in the collision.
A 75-year-old truck driver will face court later today on dangerous driving charges.
The Barrier Highway was closed in both directions but has since reopened with a 25km/h speed limit.
Cranes have been brought in from Adelaide and Port Augusta to assist in the clearing of the freight containers.
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Police anticipate the cleanup to be lengthy, as the road surface also sustained damage and will need to be inspected for safety.
9News has been told the damage bill from the crash will exceed $50 million.
The truck driver did not apply for bail.
He will appear in Adelaide’s Magistrates Court via video link today.