The death of Dan Mertzbach, 55, was described as accidental, Haaretz reported. A report said soldiers had not finished setting up the checkpoint when the vehicle approached and tried to flag the driver down using signals.
The checkpoint had been set up because of a report of a suspicious truck seen leaving one of the West Bank settlements.
An Israeli soldier was injured in the incident when he was hit by a truck driven by a Palestinian as he ran towards the Mertzbach vehicle, which had become stuck.
Mertzbach was a resident of the settlement of Otniel. He was to be buried in Jerusalem and honored at a memorial service in Otniel.