Police said in a statement that Jefferson da Silva Lima, known as Pelado da Dinya, had surrendered at the Atalaya do Norte police station in the Amazon.
Police said the suspect would be sent into custody.
Two other men are already in jail for alleged involvement in the killings: Amarildo Oliveira, known as Pelado, and his brother, Autseni de Oliveira, known as Dos Santos.
Phillips and Pereira were last seen on June 5 on their boat on the Itaquai River, near the entrance to the local Havari Valley, which borders Peru and Colombia.
On Friday, federal police said human remains found in the remote Brazilian Amazon had been identified as belonging to 57-year-old Phillips.
Additional remains found at the site near the town of Atalia do Norte have not yet been identified, but are expected to belong to local expert Pereira, 41.
“Confirmation (of the remains of Phillips) was made on the basis of dental examinations and anthropological forensics,” a statement from the federal police said. “We are currently working to fully identify the remains so that we can determine the cause of death, as well as the dynamics of the crime and the hiding of the bodies.”
The wreckage was found Wednesday after fisherman Pelado admitted killing the couple and took police to where he would bury the bodies. He told police he used a firearm to commit the crime.
The remains had arrived in the Brazilian capital on Thursday to house detectives.
The area where Phillips and Pereira went missing has witnessed violent clashes between fishermen, poachers and government agents.