Police said the third suspect, Jefferson da Silva Lima, known as Pelado da Dinha, turned himself at the police station in Atalaia do Norte in the Amazon.
Police said the suspect will be referred to a custody hearing.
Two other men are already in prison for alleged involvement in the killings: Amarildo Oliveira, known as Pelado, and his brother, Oseney de Oliveira, known as Dos Santos.
Phillips and Pereira were last seen June 5 on their boat on the Itaquai river, near the entrance of the Javari Valley Indigenous Territory, which borders Peru and Colombia.
On Friday, federal police said that human remains found in Brazil’s remote Amazon have been identified as belonging to Phillips, 57.
Additional remains found at the site near the city of Atalaia do Norte were confirmed to belong to Indigenous expert Pereira, 41, according to the police statement on Saturday.
The remains were found on Wednesday, after fisherman Pelado confessed to killing the pair, and took police to the place where he would have buried the bodies. He told officers that he used a firearm to commit the crime.
The remains had arrived in the capital city of Brasilia on Thursday for forensic examinations.
The area where Phillips and Pereira went missing has seen violent conflicts between fishermen, poachers, and government agents.