The rescue team "recovered and identified the last of the remains of the buried workers early this morning", the Indonesian subsidiary of Freeport-McMoRan said in a statement.
Thirty-eight workers were initially trapped on May 14 when part of the tunnel caved in at Freeport's Grasberg, one of the world's biggest gold and copper mines high in the mountains of remote Papua province.
Ten people were recovered alive soon afterwards but rescue efforts were hampered by the narrow tunnel and the unstable situation, with rocks continuing to fall from the roof.
"We continue to grieve with the families even as we close this grim chapter," said Rozik Soetjipto, president of Freeport's Indonesian subsidiary.
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Freeport-McMoRan president and chief executive Richard Adkerson arrived on site at the weekend to visit the injured workers and the families of those still buried.
Indonesian President Susilo Bambang Yudhoyono has pledged that the government will carry out a full investigation into the accident, and safety at mines across the country will be checked.
Operations have been halted at the mine since last week as a mark of respect for those affected by the accident.
Grasberg has a troubled history. A three-month strike in 2011 crippled production, and around the same time there was a spate of deadly shootings at the mine.