The man, Patrick Stallworth, and the woman, Derick Brown, are being held at the Jefferson County Jail without bond, Jefferson County District Attorney Danny Carr said in a statement.
If convicted, Stallworth and Brown could face the death penalty. It is unclear if either of them has an attorney.
Kamille's remains were found inside a dumpster that was taken to a landfill, Birmingham Police Chief Patrick D. Smith said at a news conference Tuesday, 10 days after the child, who was also known as Cupcake, vanished from a birthday party Oct. 12.
Smith said police had been detaining all of the trash being collected from one area for several days in the search for her.
He said at Tuesday's news conference that Stallworth and Brown would also face kidnapping charges. Authorities said Thursday the charge could still be added.
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Asked Tuesday about the suspects' possible motive, Smith said, "We believe that this was something they thought about and acted upon, and they saw an opportunity to take a young child, which they did. Our further investigation will reveal whatever actions were taken after that."
He added that investigators do not believe Stallworth and Brown knew Kamille or her family.
An Amber Alert was issued following Kamille's disappearance, and Crime Stoppers offered a $20,000 cash reward Oct. 16 for tips and information.
Frank Barefield, chairman of the board of Crime Stoppers of Metro Alabama, told reporters at a news conference Friday that the organization had received more tips in the search for Kamille than in any other case before.
"I don’t remember any time where we’ve gotten more tips or more pledges of money," he said.
Several of the more than 400 tips received were helpful to investigators and a portion of the reward would be issued to the tipsters, Barefield said. He said the amount given will not be disclosed.
"We don’t say what the tip was and we don’t talk about what the reward was," he said of the organization's policies. "Possibly divulging that information could put the tipster at risk."
Barefield, who was joined by the Birmingham police chief at Friday's news conference, said the contributions in excess of the $20,000 reward would be used to establish a Kamille Cupcake McKinney Memorial Reward Fund.
"This will provide money for law enforcement agencies with future abductions and disappearances of children," Barefield said.
Smith said Kamille's death and the intense 10-day search for her had changed not only Crime Stoppers but also the city of Birmingham.
"This 3-year-old has Herculean power," Smith said. "She’s unified a city. She’s brought people together. Some who didn’t know each other and many who didn’t know her."
Smith said the child's murder touched a chord in the city because it was a "'How dare you?' crime."
"How dare you touch our children? How dare you kidnap this child? How dare you do harm to this little girl?" Smith said. "How dare you disrespect our community? It’s a 'How dare you?' crime and 'Why did you do this to us?'"
Janelle Griffith is a breaking news reporter for NBC News.