Louis Ross and Jennifer Campbell were being questioned by investigators in the case of Hassani Campbell, who has cerebral palsy, Oakland police spokesman Jeff Thomason said.
The couple were arrested separately within an hour of each other, Thomason added. He said police have not recovered the boy's body.
"This is not a missing persons case anymore. This is a homicide investigation," Thomason said late Friday outside police headquarters in downtown Oakland. "We are talking to the people responsible. We do believe Hasanni Campbell is dead."
Thomason would not say what led to the couple's arrests or what had led police to conclude that the boy was dead.
A team of investigators searched the couple's Bay Area home again Friday for clues in Fremont, Calif.
Thomason said it's an ongoing investigation discuss further what led to the arrest after the boy disappeared on Aug. 10. Ross, the last known person to see Hasanni, said the boy disappeared after he briefly left the boy outside his car in the rear parking lot of an upscale Oakland neighborhood shoe store where his fiancee, Campbell, works.
Ross said he went to the store's front entrance to ask Campbell to open the back door, but when he returned to the parking lot, Hasanni was gone.
Hasanni is black, 3 feet tall, weighs 30 pounds and was last seen wearing a gray sweat shirt and gray pants. He also wears arches on his legs to help him walk.
After the boy's disappearance, his foster parents made tearful public pleas for his safe return that included vigils outside the shoe store and dozens of volunteers handing out fliers with Hasanni's face and holding a car wash to add to a $10,000 reward.
There's even a Web site - findhasanni.com - where his foster family tries to explain their role.
"We understand that there is a lot of speculation out there due to misconceptions about our family and the environment Hasanni was living in but to us he is a son, a brother, a family member and so much more and not just a foster child," a message from the site reads.
But, with police receiving a lack of strong tips and bloodhounds unable to detect the scent of where Hasanni allegedly disappeared, many wondered if his family had anything to do with it. Both Ross and police had said his family was cooperating with authorities, although Ross felt police believed he and Campbell, who is six months pregnant, did something wrong.
They both have denied any involvement with his disappearance.
During a second vigil for Hasanni outside the shoe store on Monday, the soft-spoken Ross told The Associated Press that "in the court of public opinion I've been charged, tried and convicted," regarding the boy's disappearance.