Identification of Mr Phillips was based on dental records, police said.
The second body, which is believed to be that of the indigeneous expert, Bruno Pereira, who was with Mr Phillips when they both disappeared in a remote part of the Amazon, is still being examined.
Mr Phillips, 57, and Mr Pereira, 41, went missing on June 5 in the Javari Valley, which borders Peru and Colombia.
Earlier this week, a suspect confessed to burying the two bodies.
“The remains of Dom Phillips were part of the material collected at the place indicated by Amarildo da Costa Oliveira,” police said.
Phillips, a freelance reporter who had written for the Guardian and the Washington Post, was doing research for a book on the trip with Pereira, a former head of isolated and recently contacted tribes at federal indigenous affairs agency Funai.
Police said they were still searching for the boat Mr Phillips and Mr Pereira were travelling in when they were last seen alive.
US State Department spokesman Ned Price called for “accountability and justice,” saying that Mr Phillips and Mr Pereira were murdered for supporting conservation of the rainforest and native peoples.
“Our condolences to the families of Dom Phillips and Bruno Pereira... We must collectively strengthen efforts to protect environmental defenders and journalists,” Mr Price said on Twitter.
On Thursday, Mr Phillips’ wife, Alessandra Sampaio said: “Although we are still awaiting definitive confirmations, this tragic outcome puts an end to the anguish of not knowing Dom and Bruno’s whereabouts.
“Now we can bring them home and say goodbye with love.”