The vessel was found at a depth of more than 800 meters, a rescue submarine from Singapore visually confirmed the find on Sunday morning after signals were interpreted on the submarine.
There was no longer any hope of finding any survivors and the authorities now state that all crew members are dead.
Ships, aircraft and hundreds of military personnel have taken part in the search since the KRI Nanggala disappeared during an exercise on Wednesday.
Since then, several finds have been made in the sea, including objects found inside the submarine.
The sea is too deep for safe salvage
Authorities have warned that a salvage operation could be both dangerous and complicated because the sea is so deep where the vessel disappeared.
Indonesian President Joko Widodo has offered his condolences to the families of the victims.
"All Indonesians express our deep sorrow over this tragedy, especially to the families of the crew members," he said in a statement.
Votes are now being raised to modernize the country's fleet, KRI Nanggala was built 44 years ago.
"This could be a lesson for the government to improve military technology and be careful about how it uses the already existing, people's lives are at stake," said 29-year-old Hein Ferdy Sentoso from Banyuwangi, where the rescue operation was based.