It happened in the southbound lanes at Second Street, sending flames and dark smoke into the sky.
The California Highway Patrol initially said the crash appeared to be due to an unsafe lane change.
Officers now tell Action News the investigation shows the box truck was disabled on the right shoulder and had been there for about 10 minutes when it was side-swiped by the tanker.
The driver of the box truck had called for assistance before the crash, but it's unclear if the vehicle's hazard lights were on.
The fuel tanker had 8,600 gallons of fuel and became fully engulfed in flames after the impact. Both of the drivers involved had minor injuries and are expected to be okay.
Officers also confirmed a third car was hit by debris from the crash. That driver was not hurt.
Some drivers turned around into oncoming traffic lanes in an effort to avoid the traffic jam early Saturday.
While the fast lane has reopened, the other lanes of southbound Highway 99 are expected to remain closed into Saturday night.