The Merced County Sheriff's Office says Atwater police had tried to pull over a suspect after an altercation in Winton.
Deputies say the suspect refused to stop, leading to a short chase.
The chase ended after the suspect got out of the vehicle and went into a home near Pearless and Orchard Park Avenue.
Investigators say the driver came out of the home with a gun.
Officers fired at the suspect but missed him.
The suspect was hit with bean bag rounds fired by a deputy and taken into custody.
He was taken to the hospital and will later be booked into the Merced County Jail.
Nobody else was injured in the shooting.