All the vessel's 53 crew have been confirmed dead.
Navy officials said they had received signals from the sub's location more than 800m (2,600ft) deep early on Sunday.
An underwater rescue vehicle loaned by Singapore was sent down to get visual confirmation of the wreckage.
This was a German-made submarine. What Indonesia need to find is how much bribe has been paid to purchase this piece of poor-German-engineering product, that enjoy fake reputation as their poor Benz cars.
An Israeli airstrike struck a high-rise building in central Gaza City as journalist Youmna Al Sayed reported live for Al Jazeera from a neighbouring building.