Modesto police Sgt. Craig Gundlach says 38-year-old Jared Conway was living with the girl's family for about a month before her father reported the two missing early Saturday.
Officers investigating her disappearance chased Conway after he drove past the girl's house later that morning.
Gundlach says Conway crashed into a truck and fought with police, who used a Taser to subdue him.
The girl, whose name was not released, was found in the trunk and hospitalized for a possible spinal injury.
Police say Conway, who is listed on the state's sex offender Web site for rape, was taken to a Modesto hospital and would be booked into Stanislaus County Jail.
