Bay Area Rapid Transit police said they took Sara Krueger, 23, and Ryan Scott Warner, 26, into custody about 11 a.m. PST at a BART station in El Cerrito a short time after the two fled a nearby restaurant where they had been spotted, the San Francisco Chronicle reported.
Napa police then arrested the pair on suspicion of special-circumstances murder and assault on a child resulting in death in the slaying of Kayleigh Slusher.
Kayleigh was found dead of apparent blunt force trauma in her bed in Krueger's apartment about 1 p.m. Saturday by Napa police officers conducting a welfare check based on an anonymous phone tip, police said.
"There is also preliminary evidence of a sexual assault," Napa police Lt. Debbie Peecook told the newspaper.
No parent or guardian was at the home, police said.