Crews worked for more than 12 hours Thursday to repair the damage on the highway near 16th Street.
The California Highway Patrol says the truck lost control in the southbound tunnel lane and overturned its back trailer.
The guardrail punctured the trailer, spilling 1,000 gallons of liquid fertilizer.
The trailer was removed, and hazardous materials crews worked to clear the scene.
The CHP says the lanes are open, but there is still construction happening along the highway so drivers are asked to be cautious.