The child disappeared shortly after his father, Aramazd Andressian Sr., took him on a trip to Disneyland in April.
Andressian, 35, of South Pasadena, California, was initially scheduled for a preliminary hearing on Tuesday, but instead changed his not guilty plea to guilty. He remained calm and serious during his court appearance.
Andressian's attorney, Ambrosio Rodriguez, said after the hearing that his client is "beyond words in regretting" his actions. Rodriguez said Andressian Sr. had given police information about where to find his son's remains.
Andressian faces 25 years to life in state prison. He will be formally sentenced on August 23.
A monthslong search
Aramazd Jr.'s remains were found in the Lake Cachuma area
of Santa Barbara County in early July. Police did not say where the remains were found or what condition they were in.
He was reported missing in April after Ana Estevez, the boy's mother, said her estranged husband did not return his son during a planned custody exchange. The boy had spent the previous week with his father.
On the day the boy was supposed to be returned to Estevez, a pedestrian found Andressian Sr. unconscious next to his car at a South Pasadena park and called police. His son wasn't there.
Andressian told investigators he had ingested a prescription medication that wasn't his own that morning, deputies said.
"He did not remember what happened to his child or any details that were useful in locating his son," Lt. Joe Mendoza of the Los Angeles County Sheriff's Department told reporters in a May news conference.
Both Andressian and Estevez made public comments over the next two months, pleading for the public to help find their son.
Nearly a week after the boy was reported missing, Andressian released a statement through his attorney. After having breakfast, he said, the boy wanted to go to the park before meeting his mom, CNN affiliate KCBS reported
"I was at the park with my son, and then I found myself waking up in Huntington Memorial Hospital hours later," the statement said. "I can only speculate that I must have been attacked in the park, given my unresponsive state and subsequent physical condition."
"My family and I are heartbroken and grief-stricken that Aramazd Jr. is missing and may be in harm's way," he added.
Andressian left the Los Angeles area after being questioned by police and traveled to Las Vegas, authorities said. He spent 47 days there, during which time he shaved his beard and dyed his hair. Police arrested him in late June
Police at the time said he was "taking part in activities and displaying mannerisms that were not consistent with a grieving parent."
In a news conference after his arrest, investigators said Andressian and his wife were going through a "tumultuous divorce
" when he took his son on a trip to Disneyland.