Authorities said the assault happened early Thursday morning.
Police said Noah Holland, 21, broke into the home, stripped naked, and climbed on top of the sleeping child in her bedroom.
"Her mother heard her daughter's screams, when she went into the bedroom the suspect was gone but evidence was left behind," said Commander Aaron Johnson from the Rohnert Park Department of Public Safety.
Johnson said the suspect ran off without his clothes.
Police won't say what other evidence was left behind but it was enough to track Holland down at home in Santa Rosa where he was arrested.
The girl and her family do not know Holland.
Police said the suspect gained entry to the house with a garage door opener found inside an unlocked car parked in the driveway.
"My heart goes out to the family and that little girl," said neighbor Teri Kennedy.
Police said the child did the right thing by screaming and hitting the suspect.
"We feel the brave actions of the victim averted a real tragedy," said Commander Johnson.
Holland's alleged burglary accomplice, 18-year-old Tristan ford was also arrested.
Police said he played no part in the sexual assault.