Navy Chief of Staff Yudo Margono said the submarine had been broken into three pieces.
"With this authentic proof, we can confirm that KRI Nanggala 402 has sunk and all of its 53 sailors have died on duty," Air Marshall Hadi Tjahjanto told a press conference.
Underwater drone images showed the wreckage on the seafloor. It was found by a Singaporean craft about 1,500 meters to the south of where it last dove.
Indonesian President Joko Widodo earlier offered his condolences to the families of those lost in a submarine accident four days ago.
He confirmed that the KRI Nanggala 402 submarine sank and that the 53 crew members are presumed to have died.
"All of us Indonesians express our deep sorrow over this tragedy, especially to the families of the submarine crew," he said.