Aramazd Andressian Sr., 35, was arrested for the murder of his son Aramazd Andressian Jr. at 1 p.m. Friday in the Las Vegas area and booked into a jail there on $10 million bail.
He is expected to be extradited to Los Angeles County.
The boy's body has still not been found, according to the sheriff's department.
Police have not disclosed what information led them to make the arrest or why Andressian was in Las Vegas. They said they had presented evidence in the case to the Los Angeles County District Attorney's Office and obtained a murder filing against the suspect.
The 5-year-old was last seen early Friday, April 21, in his father's custody.
Andressian Sr.'s estranged wife reported her son missing after his father did not drop the boy off as scheduled.
Hours later, Andressian Sr. was discovered passed out at South Pasadena's Arroyo Park. His gray 2004 BMW sedan was found nearby with its interior and exterior doused with gasoline.
He could not account for his son's whereabouts.
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He was taken into custody at that time, but he was later released due to lack of evidence.
Since that time, authorities have mounted massive search operations, scouring local parks and going as far north as Santa Barbara. They also executed a search warrant at the home of the mother of Andressian Sr. in Montebello.
A $20,000 reward has been offered in connection with the case.
The arrest was made by officials with the Los Angeles County Sheriff's Department, the Las Vegas police and the U.S. Marshals Service.
A press conference to provide more details is scheduled for Monday in downtown Los Angeles.