Julio Mejia, 39, was taken into custody Thursday.
Prosecutors claim the sexual assault took place in September while the child was a passenger in the car.
Mejia is charged with two counts of sexual assault, second degree, endangering the welfare of a child, and two counts of criminal sexual contact.
He could face up to 10 years in prison if convicted.
Mejia is due back in court on February 4.
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