Aramazd Andressian Sr., hands shackled at his waist, appeared before Los Angeles County Superior Court Judge Cathryn Brougham, who set bail at $10 million and scheduled a preliminary hearing for Aug. 16.
Authorities have alleged Andressian killed his son, Aramazd Andressian Jr., to get back at his estranged wife.
Andressian was returned to Los Angeles County last week from Las Vegas, where he was arrested.
Defense attorney Ambrosio Rodriguez said outside court that a blue smock his client wore during the arraignment was a suicide-prevention garment and that he was being evaluated by a jail psychiatrist.
Andressian is "in a state of shock," said the attorney, who declined to answer questions about the case.
Authorities say homicide detectives discovered the remains of the boy near Lake Cachuma in Santa Barbara County on June 30. He had been missing for more than two months.
"We are all grieving right now," Shaun Estevez, the boy's uncle, said after the arraignment. "We're really hurting."
He said his sister, the boy's mother, is still trying to come to grips with her son's death.
"We're here for justice for Piqui," he said, using the boy's nickname. "He was a great kid."
Estevez said "no words could describe" seeing the father in court.
Investigators think the boy was killed early April 21 after a trip to Disneyland.
Police had searched for the boy since his father was found passed out in a park in South Pasadena on April 22. Andressian had taken prescription pills and was found in a car doused in gasoline in an apparent suicide attempt, sheriff's officials said.
Andressian told authorities that he drove that day about 145 miles (233 kilometers) to Lake Cachuma. Before finding the remains, authorities had twice previously searched the lake unsuccessfully, using dogs and a dive team.