The 52-year-old was travelling back to his native Asturias when the incident happened in the early hours of Sunday morning.
Marcelino's car was making its way along a stretch of motorway between Logrono and Bilbao when it collided with a wild boar that ran out onto the road.
The former Villarreal manager had to go to a nearby hospital for observations but was later given the all-clear.
Valencia said in a statement: "Marcelino Garcia Toral was involved in a car accident early this morning, while travelling home to Asturias to spend the holidays with his family.
"It took place on a stretch of motorway between Logrono and Bilbao, when a wild boar crossed the road and collided with his car. He was taken to hospital, but has already been given the all clear."
No details have been released on the welfare of the boar.